Many atheists are keen to identify indoctrination within Christian (or other religious) communities. Not surprisingly, however, they typically fail to recognize the extent that indoctrination can occur among atheists. In this article, I am going to take a look at indoctrination in the contemporary resurgence of atheism known as "the new atheism."
I can already hear the atheist retort: "Indoctrinated?! How can an atheist be indoctrinated? After all, atheism simply is the rejection of theism!"
It is true that atheism is not a unified ideology, let alone an institution. But that does not mean that self-professing atheists are automatically exempt from the danger of indoctrination. In fact, the lack of formal institution, creed, or leader may, ironically enough, cultivate a false sense of intellectual independence and liberation among atheists that can render an individual even more vulnerable to indoctrination. What is necessary for indoctrination is not a magisterium or sacred text but simply a set of beliefs that inhibit critical thought, and in this article, I will argue that the new atheism is broadly characterized with these kinds of indoctrinational beliefs.
One of the most effective ways to inure an ideology from critical appraisal is by convincing those who hold it that it is not a set of beliefs in need of defense but rather a common-sense conclusion that should be recognized by any rational person. After all, common-sense surely needs no defense! With that in mind, it is not surprising that a number of new atheists stress that atheism is precisely nothing more than good sense. This is how Sam Harris puts it:
"Atheism is not a philosophy; it is not even a view of the world; it is simply an admission of the obvious. In fact, 'atheism' is a term that should not even exist. No one ever needs to identify himself as a 'non-astrologer' or a 'non-alchemist.' We do not have words for people who doubt that Elvis is still alive or that aliens have traversed the galaxy only to molest ranchers and their cattle. Atheism is nothing more than the noises reasonable people make in the presence of unjustified religious beliefs." 
If atheism is simply "an admission of the obvious," then it needs no defense. Furthermore, those people who are foolish enough to deny atheism are de facto standing in direct opposition to common-sense.
David Mills argues along the same lines when he observes:
"atheists have no obligation to prove or disprove anything. Otherwise—if you demand belief in all Beings for which there is no absolute dis-proof—then you are forced by your own twisted 'logic' to believe in mile-long pink elephants on Pluto, since, at present, we haven't explored Pluto and shown them to be nonexistent."
Like Harris, Mills aims to demonstrate that the atheist is not obliged to defend anything. Rather, in his view, atheism is simply common-sense. Meanwhile, theistic belief is manifestly absurd.
These convictions concerning the radically different status of atheism and theism effectively establish a powerful binary opposition between the irrational theist (or, as Richard Dawkins says, the "faith-head") and the rational atheist. And that, in turn, places core atheistic assumptions beyond the realm of serious critical scrutiny. It's critical to recognize that placing one's beliefs beyond critical scrutiny is the most important step toward indoctrination.
In this new atheist view, the religious individual is bound by the cognitive chains of irrational dogma, while the atheist-skeptic is unencumbered by any dogmas and thus is free to countenance the evidence without bias. Consequently, new atheists could hardly be more withering in their assessment of religious conviction. The depth of the binary opposition is captured in the following statement from Robert Pirsig that Richard Dawkins quotes with approval: "When one person suffers from a delusion, it is called insanity. When many people suffer from a delusion it is called Religion." Similarly Sam Harris describes "the history of Christian theology" as "the story of bookish men parsing a collective delusion." And if the notion of religion as a collective delusion were not bad enough, Dawkins also claims that religion is like a mind virus which co-opts and corrupts the mind of its host like a parasite. Thus, while the atheist is supposed to be the liberated free thinker, the religious believer is enslaved to a mass, collective delusion that borders on insanity.
Not surprisingly, given that new atheists assume that the religiously devout suffer from a cognitive delusion, the reflections of religious people on metaphysical questions are to be taken with no greater seriousness than the mental patient mumbling in the corner of the sanatorium. With this assumption, atheists can dismiss with staggering glibness the entire discipline of theology. For instance, Dawkins refers to the ontological argument for God's existence, an argument that has fascinated many of the most astute philosophical minds for the last eight hundred years, merely as "infantile." Moreover, he claims that "the notion that religion is a proper field in which one might claim expertise, is one that should not go unquestioned. That clergyman presumably would not have deferred to the expertise of a claimed 'fairyologist' on the exact shape and color of fairy wings." Needless to say, it is a waste of time to get into a debate with somebody who insists on the existence of fairies (even if they happen to claim expertise in those matters).
In the paperback version of The God Delusion Dawkins responds directly to the charge that he had been inappropriately dismissive of theology. In reply, he writes: "I would happily have forgone bestsellerdom [in The God Delusion] if there had been the slightest hope of Duns Scotus [a medieval Christian theologian] illuminating my central question of whether God exists." Needless to say, Dawkins assumes that there is literally no hope that so eminent a theologian as Duns Scotus (the famed "subtle doctor" of the thirteenth century) could have anything enlightening to say on the question of God's existence.
These sharp binary categories — enlightened atheist vs. irrational Christian — are effective for perpetuating atheistic indoctrination, for they allow even the most novice atheist to dismiss the most senior theologians as deluded fools and irrational know-nothings. So we have David Mills, commenting: "Nor, in my opinion, is it even possible to change the religious views of those who perceive themselves as ethically superior because they belong to the one 'true' religion. Their ears and eyes and minds are closed forever. No amount of science or logic will make any difference to them." Note how Mills categorically dismisses anybody who assents to a formal religious faith as hopelessly beyond the reach of rational argument. Other examples of this strategy of marginalization are easy to find.
In his bestselling book, God is not Great, Christopher Hitchens asserts, "Religion comes from the period of human prehistory where nobody . . . had the smallest idea what was going on." This sweeping statement allows Hitchens to conclude that "all attempts to reconcile faith with science and reason are consigned to failure and ridicule." So the same binary opposition that enables Dawkins to dismiss theologians as idiots empowers Hitchens to ignore anybody (scientists included) who would seek to reconcile science with religion. You might as well attempt to reconcile science with alchemy.
We certainly find ample evidence for the first two dimensions of indoctrination in the new atheists given their dichotomy between "irrational faith" and "reasonable common sense". But there is one final factor that is especially powerful in perpetuating indoctrination: the perception of a crisis situation. In short, the person facing a crisis is more apt to set aside careful nuance and embrace the security and order of stark binary categories. And that is definitely the case with teh new atheism.
To begin with, we need to understand that the new atheism is a post 9/11 phenomenon spurred on by the fear that the unchecked growth of religion will lead to increasing violence, intolerance, and oppression. This crisis justifies the new atheist in adopting a new level of stridency against religion. Dawkins thus explains his animus toward religion like this: "[S]uch hostility as I or other atheists occasionally voice towards religion is limited to words. I am not going to bomb anybody, behead them, stone them, burn them at the stake, crucify them, or fly planes into their skyscrapers, just because of a theological disagreement."
Critics of religion like Dawkins appeal to this fear of imminent violence and oppression arising from the teeming hordes of the religiously devout as the justification for forgoing nuance and charity. (You don't mind your 'p's and 'q's when you're in a life-or-death struggle with the glazed-eyed religious zealot.) At the beginning of his book Breaking the Spell (the spell being religion), philosopher Daniel Dennett provides a revealing admission: "Perhaps I should have devoted several more years to study [of religion] before writing this book, but since the urgency of the message was borne in on me again and again by current events, I had to settle for the perspectives I had managed to achieve so far" (emphasis added). So presumably Dennett's often blunt treatment of religion should be excused because he did not have the luxury of more in-depth study, given the state of crisis posed by fundamentalism.
The predictable result of new atheist indoctrination is an inability to take the views of the religiously devout person with intellectual care and charity. We find ample evidence of this in Dawkins' book The God Delusion. For instance, Dawkins described his puzzlement with religiously devout scientists as follows: "I remain baffled, not so much by their belief in a cosmic lawgiver of some kind, as by their belief in the details of the Christian religion: resurrection, forgiveness of sins and all." Nor can Dawkins understand those theists who believe God could have used evolution to create: "I am continually astonished by those theists who, far from having their consciousness raised in the way that I propose, seem to rejoice in natural selection as 'God's way of achieving his creation.'" Dawkins is even mystified that some Christians could actually be highly educated: "Why any circles worthy of the name of sophisticated remain within the Church is a mystery at least as deep as those that theologians enjoy." Dawkins' mystification carries over to the high levels of religious observance within the American population: "The religiosity of today's America is something truly remarkable."
Note the terms I italicized in these quotes: baffled, astonished, mystery, remarkable. In these less-than-subtle ways, Dawkins marginalizes the religiously devout person as a bizarre phenomenon that resists rational explanation. And this incomprehension, this inability to understand people on the other side of your comfortable binary framework, is a result of indoctrination.
Over the last fifteen years, I have engaged in extensive dialogue with atheists through written and spoken debates in books, blogs, radio and podcast exchanges and formal university debates. In that time, I have encountered a number of thoughtful and reflective atheists. But I have also encountered a disturbing number of atheists who reflect this same inability to engage with the Christian person with intellectual sophistication and charity. As one atheist candidly put it in a crass question to me following an apologetic presentation: "how old were you when you were first indoctrinated?" That is what the indoctrinated atheist mindset looks like.
Note: This article is adapted from a section of my book You're Not as Crazy as I Think: Dialogue in a World of Loud Voices and Hardened Opinions.
 The new atheism is a strident, anti-religious form of atheism that has emerged as a force in popular culture since 9/11 and which is represented by its four leaders, Richard Dawkins, Daniel Dennett, Sam Harris, and Christopher Hitchens.
 Harris, Letter to a Christian Nation (New York: Alfred A. Knopf, 2006), 51.
 David Mills, Atheist Universe: The Thinking Person's Answer to Christian Fundamentalism (Berkeley: Ulysses, 2006), 29.
 Barbara Ehrenreich, "Give me that new-time religion," Mother Jones (June/July, 1987), 60.
 Cited in Dawkins, The God Delusion (Boston: Mariner, 2008), 28.
 Harris, Letter to a Christian Nation, 5.
 See "Viruses of the Mind," in A Devil's Chaplain: Reflections on Hope, Lies, Science, and Love (New York: Houghton Mifflin, 2003), 128-151.
 Dawkins, The God Delusion, 104.
 Dawkins, The God Delusion, 37.
 Dawkins, The God Delusion, 14.
 Mills, Atheist Universe, 21.
 Hitchens, god is not Great: how religion poisons everything (New York: Twelve, 2007), 64.
 Hitchens, god is not Great, 64-5
 Not to be outdone, Sam Harris claims that "the central tenet of every religious tradition is that all others are mere repositories of error or, at best, dangerously incomplete. Intolerance is thus intrinsic to every creed." The End of Faith: Religion, Terror, and the Future of Reason (New York: Norton, 2006), 13.
 Dawkins, The God Delusion, 318.
 Dennett, Breaking the Spell: Religion as a Natural Phenomenon (New York: Penguin, 2006), xiv, emphasis added.
 Dawkins, The God Delusion, 125, emphasis added.
 Dawkins, The God Delusion, 143-144, emphasis added.
 Dawkins, The God Delusion, 84, emphasis added.
 Dawkins, The God Delusion, 26, emphasis added.