I have to confess, when I heard they were making a movie out of The Golden Compass -- the first novel in Philip Pullman's His Dark Materials sequence -- the anti-religious themes in the book were the first thing I thought of. The comments on this post on Friendly Atheist feature a few comments that suggest that the Christian response is an over-reaction. If so, it was an entirely predictable one, for Pullman is an atheist, and he did write these books with criticism of religion in mind. On the other hand, this post on Beliefnet by Donna Freitas, a defence of His Dark Materials from a Christian perspective, speaks of the way Pullman's story can be read as affirming the religious principles on which some people build their lives. That I did not predict -- but it does not surprise me so very much.
The atheism of His Dark Materials is actually somewhat equivocal. In the fictional multiverse of the books, the Authority known as 'God' is an imposter who did not create the universe, and who is destroyed almost incidentally in the third book by the main characters without their even knowing it. It's almost a throw-away scene, one which, if the third book made it to the screen, might be cut simply for reasons of time. Unlike the depiction of the Fall from Eden as a very good thing (which, certainly, some Christians might find hard to swallow) the death of 'God' is actually not that major. However, while the books reject this authoritarian imposter of a God, they do also have an overarching notion of destiny and purpose, embodied in a mysterious substance known as 'Dust'.
What is 'Dust'? The book gives several possible answers: original sin, the human spirit, a substance attracted to an adult's conscious mind and engagement in life. For an atheist, giving this somewhat humanist idea a supernatural tilt is hardly terrible because this is a
fantasy book. A Christian, however, might see a hint of some true God in this idea, a God who affirms human beings in contrast to the authoritarian religion which crushes them. His Dark Materials reads to me like a humanist freedom cry, a blazing beacon of joy in experience, a command to live life richly and fully, unstifled by repressive religious notions. There are more than a few Christians who value some of the same things as humanists, so we should not be surprised that they also find value in these books.
I'll say this outright: Pullman's His Dark Materials sequence definitely strengthened my atheism. It made me much more likely to see certain types of religious notions (such as giving all control over to God, or such as the repression of sexuality) as antithetical to a life well lived. But if you do believe in God, Pullman's books won't necessarily seem to be fighting that notion overmuch. It really depends what sort of God you have.