Kevin Drum gets this about right:
I’m not in the habit of defending the Religious Right, but I have to say that [with regards to The Golden Compass] they have a point. I’m sure the movie itself will indeed be harmless, but the books are every conservative Christian’s nightmare of what the secular left’s real agenda is — assuming you get past the first two volumes, that is. Pullman’s attack on Christianity is foreshadowed in those books, but in the third it’s laid bare with no attempt at even unsubtle Narnia-esque analogies. The Amber Spyglass is the story of how God (yes, the God of Abraham, the one in the Bible) has ruled despotically and malevolently over the Earth for 30,000 years and the forces of good and decency are finally going to kill him. And they do.
I read the three His Dark Materials books when I was ten, and loved them. Not because of the fantasy – I hated the Narnia books, and the Harry Potter books, and Tolkein, and pretty much all other children’s fantasy books – but because they were overtly political, and their militant atheism was a large part of that. Compared to the other stuff I was reading as a fifth-grader, dramatic battle scenes pitting anti-theist armies against God were pretty potent. Reading about covert operatives swooping into Hell to free its denizens from God’s imperial grasp was pretty powerful. Where the themes of the early Harry Potter books and Lord of the Rings amounted to “evil bad!”, and the Narnia books read like Sunday school with swords, His Dark Materials was much more interesting. It was new. It was dangerous. And that’s why I liked it.
So Kevin’s right: the books should threaten the religious right, as kids reading them are likely to start questioning what they’ve been taught. And the religious right’s faith is sufficiently vulnerable that a handful of children’s books are enough to threaten it.