As I talked with him and asked him what his doubts and troubles were regarding his Catholic faith, it became clear to me that he really didn't have a true understanding of what Christianity is, and more than that, what the basis of religion actually is and why people believe in God. For a barely twenty-year-old this isn't surprising. What was being shaken in his mind wasn't true faith in God and Christianity, but rather his uninformed view of God and Christianity; a worldview inherited from his parents without personal discovery and genuine understanding. Of course in his mind he thought he understood religion and had found it flawed. I shared with him that I thought it was good, healthy and normal that he was questioning his upbringing, but that he needed to see that his understanding of religion was inadequate and that for him, religion needed to be reexamined, not simply repudiated.
I believe that this is true for so many. Being raised religious doesn't mean that a person really understands religion, and in all likelihood it can be one of the greatest factors of not understanding religion. Parents do not always equip their children for facing the questions of life. Sometimes children are just taught wrongly, or sometimes they are taught true conclusions without being taught why those conclusions are true. When people think they know what religion is when they don't, once their faith is shaken they may fail to see that the faith-crisis in not due to the inadequacy of their religion, but rather due to the inadequacy of their own understanding of religion. And I say this about many religions, not just Christianity. I believe that Hinduism, Islam, Mormonism, etc. are all stronger and more reasonable worldviews than atheism. But many people are drawn into atheism, usually early in their lives, because they failed to really grasp what religion is.
"A little philosophy inclineth man's mind to atheism, but depth in philosophy bringeth men's minds about to religion." (Francis Bacon)
It has been recognized for a very long time that many people become atheists, not for intellectual reasons, but for emotional/psychological ones: i.e. bad experiences in religion (where there is no shortage!), or to escape from guilt, or because of anger and confusion at God for allowing some thing to happen. Not only is this is an irrational move (although an understandable one), it too, I think, is based on failing to rightly understand religion. In the first place, the basis of religion is not emotional nor pragmatic--that it makes you feel good and gives you deliverance from bad experiences (which we, of course, all want, and not wrongly)--but its basis is really intellectual. God is believed in because believing in God is reasonable (more reasonable than to not believe in God). Come what may, people believe in the existence of God because there are things that now exist that declare God's existence. Of course, this conviction comes with emotional and practical implications, but it is the conviction that is the basis and not the results of the conviction. This persistent little fact indeed opens the floodgate of a whole host of difficult questions and theological problems, but it is precisely this fact of the intellectual basis of religion that explains the permanence of these questions, and explains why humans--even atheists--have a terrible time simply walking away.
But going further than this, as Christians we say that faith in who God is gives us the strength to face all bad experiences--including our own guilt--and that the solution to the pain of these things is not to escape away into irrationality and atheism (which really does provide some temporary comfort), but to take our comfort from the truth of who God is. The God of the Bible is comforting. "Comfort, comfort my people, says your God." (Is. 40:1) While some comfort may be gained by running from God, greater and lasting comfort is to be gained in knowing God. This isn't a sugar-coated view of life, for bad experiences really do happen and guilt is acknowledged as real, not ignored, but through God we really become "more than conquerors through Him who loved us." (Rom. 8:37)
Like this young man, the 21st century world needs to realize that religion needs reexamination, not repudiation. I believe it will realize this, and actually is already showing signs of realizing it.