"Pastor Wilson wants to claim that basing knowledge on reason is question-begging in the same way as basing belief in the bible on the bible itself is question-begging."

He's merely addressing foundationalism, that is, the philosophical postulation that every philosophical viewpoint must have a foundation of its own. Thus when a person is claiming to speak in the name of "Reason", he's doing no better, categorically speaking, than speaking in the name of "The Bible". He's being technical there, and he's obviously right, irrespectively of the sheer emotional punch that such a remark may or may not give to the unaware. Because all you do when defending reason against the bible is either positing another god (Reason! Roar! Thunder!) or pounding the table.

Thing is, Christopher doesn't sound as a Realist to me, as in, a person that believes that anything meaningful can be said about the "Reality". He says as much when he mumbles about "truth", and tells that the search is what is important, and we should be very skeptical of anyone speaking in its name. Chris is no "foundationalist", that is, he doesn't have to believe in any "eternal" foundation in order to try and build the building of knowledge. This is why Wilson pounds on him about this subject. "But we have to base our knowledge and reason in something".

It's a very interesting philosophical innuendo around metaphysics, noumena, relativism and absolutism. Wilson is very honest and the movie can be good.