Well, no. Sorry, but no. His words were "Religion--in particular fundamentalist religion--makes you stupid."

Not "only" fundamentalist religion, or "by which I mean" fundamentalist religion, or even "mainly" fundamentalist religion. Fundamentalist religion is a particular example, in his view, but he included all religion in his comment. It's a fairly unequivocal statement.

And military training teaches one to believe unquestioningly in authority. Does that make soldiers stupid?