I finished reading Pullman's final book in the His Dark Materials trilogy - The Amber Spyglass. Allow me to say this. Pullman is an excellent writer. His stories are wonderfully told. The characters are engaging, and the plot certianly clips along. He has a powerful imagination.
But he is dealing with very heavy subject matter here to be calling his books "young adult" fiction. I can totally see why organized religion has a problem with his books. (And if I'M saying that, you know it's true. I'm pretty moderate, I think.) Organized religion, in this trilogy, is the enemy/villain. God himself, and his cadre of angels, are the characters that the protagonists fight against (and defeat). While I think these books can be fruitful reads for adults, as they stimulate thought on topics not traditionally entertained (much like Sophie's World, which I really enjoyed), I would not want my, say, 10-year-old kid reading this stuff. It's hard enough trying to teach your child to comprehend the immensity of the world, God, faith, good/evil, without Pullman undoing all you've tried to instill.
Sooooo, if you're interested in theology, and you're over 18, read these books. If you're part of the elementary-school set, though, you might want to talk with your parents about them first.