In the following video, Dr. Robert Morey picks apart the movie Religulous. I think any atheist should consider what Dr. Morey has to say about the subject.
I think one of the most frequent problems for atheists is that they have trouble finding true Christianity. The place to find it, in its purest form, is in the Bible. If you are an atheist, and you want to know what Christianity is, pick up a Bible (KJV is a great translation, but if you cannot handle the archaic declensions and conjugations, the NKJV, ESV and NASB are also reasonably accurate English translations).