Many people operate under the naive assumption that atheists base their views on reason while Christians base their views on faith. In reality, it is just the opposite. Atheists place their faith in their limited human understanding while believers have by God's grace reached a higher level of knowledge regarding God and spirituality. Christians base their confidence upon knowledge and facts. I will call this higher level of knowledge "sanctified reason."
Think of apologetics and human reason and evangelism as taking place at the base of a mountain as logic and human reason and the Gospel get presented to unbelievers. Think of Christian faith as being that thing which brings a person halfway up the mountain through Christian conversion when the Gospel is accepted. At that level, the mystery of the cross becomes clear and the new Christian now has sanctified reason. This sanctified reason cannot be understood at the base of the mountain because "the man without the Spirit does not accept the things that come from the Spirit of God, for they are foolishness to him, and he cannot understand them, because they are spiritually discerned." (1 Cor. 2:14) Think of the top of the mountain as being heaven where we as believers will have our highest level of reason which I will call "heavenly reason." "Now we see but a poor reflection as in a mirror; then we shall see face to face. Now I know in part; then I shall know fully, even as I am fully known." (1 Cor. 13:12)
As atheists look up the mountain to Christians, it is impossible for them to know what Christians know unless they first believe in Christ for the forgiveness of their sins. "Did you receive the Spirit by observing the law, or by believing what you heard?" (Galatians 3:2) When the gift of eternal life is received through faith in Christ, the converted soul immediately receives the Holy Spirit and the sanctified reason which He gives to God's children. This is why so many Christians know that heaven is their eternal home. This certainty is based upon sanctified reason which the Holy Spirit gives a believer through the promises of God's Word. "I write these things to you who believe in the name of the Son of God so that you may know that you have eternal life." (1 John 5:13) "Faith is being sure of what we hope for and certain of what we do not see." (Hebrews 11:1)
D.L. Moody said, "Faith is like the root; assurance is like the flower." Some believers have the flower and never doubt that heaven is their eternal home through Christ. Other believers with only the root struggle with doubt about their eternal salvation. "He who doubts is like a wave of the sea, blown and tossed by the wind." (James 1:6) Our spiritual adversary uses doubt to tear at the faith of weak believers whose grasp on the Gospel is shaky and still forming into a solid foundation. God accepts us of course and loves us unconditionally even when we as His children struggle with doubt, but He never promotes doubt because of where it leads a person.
It is dangerous to suggest to a believer that doubt and skepticism are a God-ordained aspect of faith. Those believers who are weak in faith can be pulled even further from any assurance of their salvation if they accept that premise. That is one step closer to having no faith in Christ. Isn't this what we see in some mainline denominations today and in some "Emergent" churches? There seem to be a lot of skeptics in many of those churches. They elevate the value of doubt and they mock the value of spiritual certainty. When a person is in doubt and is lacking in sanctified reason, he finds comfort in getting others to also doubt God's Word and God's promises. It makes him feel more secure to have others doubting with him. This results in the blind leading the blind. They view the notion of "absolute truth" with scorn and contempt. "The message of the cross is foolishness to those who are perishing." (1 Cor. 1:18)
As believers look down the mountain at atheists and unbelievers, we are never to "look down on them" in terms of viewing ourselves as being superior. What is superior is the sanctified reason that God gives us in His Word. "Jesus opened their minds so they could understand the Scriptures." (Luke 24:45) If you are halfway up the mountain, rejoice in what God has shown you in opening your mind to understand the facts of eternal salvation. You didn't deserve to be given this knowledge, but God in His grace has revealed the truth to you. Remember this when those at the base of the mountain look up to you and sometimes even get angry and impatient with you. They don't get it because their faith is in themselves and in their human reason. Ask God to work humility in their hearts to repent of their sin and to call upon Jesus for salvation. Who knows - you might just have a former atheist looking at you eye to eye one of these days. If God can save you, He can save anyone!