
The Golden Compass is the first book in the
His Dark Materials, a trilogy written by Philip Pullman in the 1990's. These books have been called the "atheist's"
Chronicles of Narnia because of the combination of fantasy and religious philosophy that drive the story.
His Dark Materials is essentially about the triumph of human knowledge and strength over a divine creator, who happens to call himself "God" (although he is not the actual Creator of the Universe). The characters in the books struggle against the oppressive regime of "The Church" in their world as well. In many ways, the trilogy is a sort of modern, alternate-universe take on Milton's
Paradise Lost, in which "rogue angels wage war on Heaven" and man commits Original Sin. From Pullman's perspective, human beings have been wrongfully indoctrinated that desire and knowledge are "sinful," when really they are the qualities that we should strive for the most.

Pullman himself stated in an interview that he doesn't see any atheistic agenda in his novels, but that they "promote... the good qualities of kindness, courage, curiosity, and open-mindedness." Pullman is also not an atheist, but an agnostic.
Besides fantasy and theological elements, the trilogy also contains quite a bit of particle physics and even philosophy, which includes references to the I Ching.
The Golden Compass film is somewhat similar to the book, but the makers decided to leave out or alter some of the important themes of resisting organized religion and the glorification of human knowledge over "the divine." In this way, the movie is actually a very "watered down" version of the book, since a person could see the movie and not detect even the slightest hint of an atheistic, or even anti-organized religion message.