It is my own paranoia. Here are things I remember about him that is suspicious:
1. He has a suspicious way of defining his worldview on the media. e.g. On Colbert Show he calls himself agnostic with a very weird body language. On further questioning by Colbert he said in a more awkward manner he is an atheist-without-balls, so that people would assume that the weird body language while talking about his agnosticism was because he was a closet atheist. But I think the second cover up act was to prevent from people finding out his real world view, which is in fact pro- Christian. If he is lying about his agnosticism/atheism, I bet he justifies his pretense by resorting to something along the lines of how he is doing it for the final good i.e. win more souls for christ OR defame atheism.
2. On the Infidel Guy podcast, he got into a little debate with the host and claimed that the New Testament jesus was historical. He argued this in a way that sounded very much like a Christian apologist i.e. by shifting the argument to whether Paul really wrote the Galatians (Paul claims he met James the brother of Jesus). But in fact host was asking whether the gospel legends of Jesus where historical.
3. In his book Misquoting Jesus, he gives tools that can be used by Christian apologists against claims made by atheists against Christianity. For example, he says verses that deny equal rights for women (which is used by us atheists as an example of lack of morality in the New Testament) where added later by scribes who had different agenda and was not part of the original text. It is easy to see how Christian apologists will later use this argument from an "atheist" in their favor claiming the original text of New Testament was divinely inspired. In conclusion, he is making it easy for the opposite side by working from within. I know this is plainly paranoia.