Gibson's character doesn't doubt the existence of God, but doubts that God is looking out for humanity due to what appeared to be the meaningless death of his wife. By the end of the film after he's been a witness to all the various events and coincidences that lead up to him saving his family...
Ebert and Roeper have given the film two thumbs up - they genuinely seemed to enjoy it on all sorts of levels. Did anyone catch the episode where they reviewed this movie? Aside from this film and their Country Bears review, they seemed to be at each other's throats while discussing the other...
Can't help but have exceeding high expectations for this film (a very bad thing) - I thought The Sixth Sense and Unbreakable were fantastic pieces of work that stand up extremely well to repeat viewings. I'm also glad to hear that Signs will actually come to a conclusion that fits all that comes...