Much of my undergraduate degree in philosophy was reading medieval texts (and later) from Christian philosophers, and I agree - most atheists I've encountered just don't understand the philosophical underpinnings. I *think * Dawkins circa The God Delusion is one of these, but I haven't read the book and my impressions are likely colored by my teachers and friends in undergrad who were largely sophisticated Christians.

That being said, most Christians don't seem to understand these underpinnings either.