I’m sorry to hear about your son and will keep and you in my prayers.
I was once in your son’s shoes. I went to college and had a class with an atheist teacher and readings. I held out as long as I could, but eventually caved. It is hard to tell what caused me to cave, but I think it was a mixture of sin and pride. My teacher was one of the most prideful people I have ever met; he was one of the sad cases of a person who is so smart that it is hard for them to understand that he is still human, and like the rest of us, has a mind darkened by original sin.
I came out of my quasi-atheist phase when I finally admitted to myself that I was denying/ignoring things that I knew to be true (such as miracles). I realized that I could not pretend to be both atheist and honest, so I guess honesty finally won out.
A couple things I’d say to you; pray about them and take them with a grain of salt.
If I were in your shoes, I’d do the following things:
Live as saintly life as you possibly can, including taking some time to serve others in a way that your son will see. You want to become as winning a Christian as possible, so that you can preach without saying a word. And of course, pray for your son.
Demonstrate open-mindedness by actually asking your son for recommendations. Read the things he is reading, doing your very best to find that which is true and separate it from that which is false. If you have questions about what an author means, ask your son. Establish a dialogue. Try to get your son to understand the intellectual traditions that provide the historical context for each writer. None of these people are writing in a vacuum.
Try to find a patch of common ground with your son: truth. Tell him that you respect his desire to know the truth and you have that in common with him. Tell him that you suspect that there is some truth in the books he is writing, but that you would be surprised if there are not also errors mixed in. (Ask if your son agrees. If he does, ask him to identify weaknesses in the arguments. If your son was anything like me, the books he reads gave me the occasion and the identity of an atheist, not really that many convincing reasons. Some of these writers died insane, after all.)
If you can, critique the books he is reading in a generous and charitable way, but don’t share the critiques unless he seems genuinely interested. Try to critique the books on their terms, not your own. After all, you wouldn’t critique a cookbook by quoting bible verses. Try to ask what the point of the book is, what does it assume, what conclusions does it try to argue, is it successful? Perhaps some of the books don’t even attempt to prove the atheistic position your son is adopting.
Apologize to your son that he was not given the ammunition he needed to know how to answer these atheistic attacks. When I got to college, I realized that all my Catholic upbringing didn’t even let me know that I would be attacked in this way, much less prepare me to deal with these attacks. It does less good at this point to try to share basic Catholic apologetics at this point. Apologize that his Church, etc. failed him. But point out that they failed him by not sharing THE ANSWERS TO ATHEISM. The point: there are answers! If he is not interested in reading them, then he is certainly not, by definition, open-minded. You might try to get him to question his confidence in his new world-view if he doesn’t think it can stand the critique of a Catholic defense such as the recent Scott Hahn book: Answering the New Atheism.
Ask him, point blank: Are you being honest? Deeply honest? Are you really convinced by the arguments you are reading, arguments that are helpless to explain so much of reality (such as miracles, healings, etc.)? Or are you really feeling lost? Point out that atheism is the most dismal possible world-view imaginable. If he really believes it is true, that is one thing? But, does he really believe it? Really?
Unfortunately, sin is a real problem, especially the types of bad decisions he has made by moving in with his girlfriend. But, it is probably true that the weaknesses of the church your son grew up in might have made it easier for him to fall away. I remember looking around the church when I was falling away and thinking that if these people really believed this, they would really be acting differently. (I eventually had to admit to myself that I had know idea about what was happening spiritually in these people’s souls. Again, I had to be HONEST that even I myself probably only look lukewarm even though I was very enthusiastic about my faith.) It is possible that your son’s atheism might reflect a certain sensitivity to the lack of faith that seems to run through many parishes. Only God knows the causes of your son’s atheism, and I never judge atheists because they so often embrace a position that is not far from our own moments of faithlessness. This is where being an open listener and non-judgmental is important. Always let God be the judge. Our job is always to be passionate lovers of each other and of the Truth who is Jesus. If your son wants the Truth, he can have Him! Just try to get him to relax about it and be honest with himself.
Have hope. After not too long, I realized that I had embraced pride and sin and had lied to myself, and I quickly asked God to send me someone who could inspire me back to the innocent (but not uninformed) faith I once had in high-school. I met a sweet Baptist girl who eventually became my wife. (She’s also now a Catholic!) I am in love with Jesus and his Church, and I am active in Catholic apologetics. (Check out my blog at readywithareason.blogspot.com. Send me an email if you’d like my perspective on any of the books your son is reading. I’m thinking about doing some blog posts on atheism and would love to make contact with some folks who are struggling with these issues.) Ultimately, it is important that you never lose your own sense of joy and hope.
I’ll pray for you and your son! (And don’t forget to take the above with a grain of salt! I’d really pray about some of the suggestions before acting on them…)
May St. Michael protect you and defend your son.