I think you have to give C.S. Lewis some credit. He's got an argument against naturalism that in my view is challenging. Maybe I'm a bad atheist/agnostic, but I have to admit I see force in some theistic arguments.
Here's this argument from C.S. Lewis, and it was used in a debate recently by David Wood (who has banned me from his blog).
The argument goes like this (more details here if you're interested). Let's assume naturalism is true. Our brains are the product of natural selection. So why do we have cognitive capacity? Is it because our cognitive capacity leads to truth? No. That's not what nature selects for. It's simply because our present cognitive capacity apparently has some sort of selective advantage. It makes us more successful in passing on our genes. If that is true, why should we trust that our cognitive capacity leads to truth? If it was advantageous from a natural selection perspective for us to believe that pigs have wings then that's pretty much what we should expect we would conclude despite the fact that this doesn't correspond to reality.
So if we believe naturalism is true and we believe that natural selection explains the origin of species we undermine our ability to know that our logical capacity leads to knowledge of truth. Is that conclusion right?
Well, I've been hanging out with atheists for a while, and I can't help but say I just have not heard a satisfactory answer. Some think this is an easily dismissed challenge. I don't think so. This is a blog and I can change my mind at any time. My thinking is always a work in progress. My conclusion today though is that the theist is right.
So now what? Does this make me a theist? Nope. Here is how I respond (today).
I can't know that my logical thinking leads to true conclusions. I can't really trust my own atheistic/agnostic beliefs. I believe these things due to natural selection. Or at least that's what I think. Even that thought was determined by natural selection. It could be wrong and I could never know because what I think is basically determined by these natural factors.
So what do I do? Here's what I do. I follow scientific methodologies. But why? Wasn't I determined to conclude that scientific methodologies lead to truth? Yep. And I could be wrong. But what I can say is that based upon my own experience I conclude that it is better to follow these methodologies. It seems to lead to less destruction and pain. We've tried believing in witch doctors and priests. That lead to certain results. Through scientific methodologies we've been able to abandon that way of thinking and adopt a new way, and I prefer it. So I hold to the scientific method. I can't prove that it leads to truth. What I can do though is say some conclusions are based on scientific methodologies and logic and others are not. I will be accepting the former. If you prefer another method that is your choice. In the end though scientific methodologies just work better and that's about all I can say.
So when I say that a claim is "true" what I really mean is that a conclusion is logical or based on scientific methodologies. False claims are the reverse. Naturalism and atheism are logical and scientific. Theism is not. Is naturalism true in the sense that it corresponds to reality? This we cannot know. Being logical and scientific is the best we can do. But believing these things may be entirely false and yet nature has selected for a species that has come to this conclusion. If that's the case we can never know.