As I'm sure you've heard, there's been much-publicized protest over the movie and the books. Some Christians believe it's too athiest (author Pullman has said some very negative things about the Church) and some athiests believe it doesn't go far enough in its criticism. I think the teens and pre-teens at whom this movie is aimed get it. It's about doubt and struggle and the world not being as clean and hopeful as we want it to be. Teens are often in the midst of figuring out who they are, what they believe, and who this God is; a movie or book that challenges them to think through these things is a win.
I've just started reading Generous Orthodoxy by Brian McLaren. He's a big name in emergent church circles and this book is a classic of the genre. In his introduction to the book he writes,
A friend of mine tells me it is a mistake to challenge readers to think because most readers simply want to hear what they already know and agree with, expressed with minimum personality and maximum blandness. I would probably do this if I could because those books seem to sell best, and I have kids in colleges with high tuitions. But another friend told me that learning is not the consequence of teaching or writing, but rather of thinking. So a playful, provocative, unclear, but stimulating book could actually be more worth your money than a serious, clear book that tells you what to think but doesn't make you think. (27)
We become better, more thoughtful people when challenged to think on our own rather than told what is truth. The Magisterium characters in the movie and the book talk quite a bit about how people can't be expected to know for themselves what's right and must be told. They say that the entire system (or Church) will fall apart if people thought for themselves and came to their own conclusions. Interestingly, this is precisely the argument put forth by people who were opposed to The Da Vinci Code and The Golden Compass.
Let's be clear--certainly there are dangerous ideas out in the world and certainly a large number of folks are willing to just accept them without thinking--we don't have to accept things at face value. Our own discomfort can tell us something about the world and our relationships. When we try to protect our brothers and sisters from challenging and upsetting fiction, we do them a disservice in not allowing them to think through the question themselves. One reviewer of the movie quoted the Catholic News Service: "rather than banning the movie or books, parents might instead take the opportunity to talk through any thorny philosophical issues with their teens." And I suggest starting with the books.
EDIT: A parishioner sent me this link to a beliefnet article on the positive aspects of The Golden Compass.