Everything I have read, clips of him, podcast, etc..he comes off as the exact opposite.
I have seen videos where he was asked directly if he was an atheist and he basically said that he doesn't consider himself anything like that. He isn't religious, but he just doesn't think about it. None of that matters to him. All he cares about is the advancement of science.
If anyone watched last night's episode and got offended from a religious perspective, it's because they choose not to believe in evolution. He did bring up a few topics that Intelligent Design proponents use as an argument against evolution, but it was needed. I have heard the argument that the eye is a clear indication of a designer too many times. The show shot that notion down with a very in depth and interesting segment. But he never said ID was a religious opinion or anything, just that ID was wrong. If anyone is offended by NdT looking in the camera and saying that evolution is a fact, then they just have their head in the sand.