It’s anti-God and anti-church. In fact, in the last book of the series God is killed and the people are happy because they can do whatever they want.

The film focuses on a young girl’s journey to free children from an evil organization. Critics claim the evil organization is a thinly-disguised comparison for the Christian church.
“The Golden Compass” is based on a children’s book of the same name by author Philip Pullman. However, some fear the message is anti-God.
[…]
Philip Pullman is a self-professed atheist. The author has gone on record saying his trilogy of books, called “His Dark Materials,” promotes his lack of belief in God. He said it’s his response to “The Chronicles of Narnia.”
[…]
Leading the charge against Pullman’s work is the Catholic League, which has called for a boycott of the movie because it believes “the film is bait for the books.” The Catholic League said the movie has been watered down to fool parents into thinking it’s safe to buy the books for their children.

When we saw the trailer for the movie we were looking forward to seeing it but I found out that it was anti-God and the makers of the movie were trying to downplay that aspect of the film. I was debating taking my daughters to the movie but not telling them about the underlying message unless it was blatantly obvious until my 15 year-old told me that she didn’t want to see the movie because they kill God in the book (her grandma sent her an email alert about the film). She turned her sister against the movie and now neither of them want to see it. If I want to see it, I’ll have to go by myself (which is a little pathetic, going to a children’s movie by myself) or wait to the DVD comes out (she’ll only watch it if we rent it from Redbox since it’s only $1 — she doesn’t want them to profit from their anti-Christian movie). I would be interested to see if it was obvious that the movie is anti-Christian and what a message of the rejection of God looks like. I thought my daughters would benefit from engaging other points of view and I wanted to see how they would react to a challenge to their faith.
Yeah, I’m not afraid of the film or losing my faith and I’m not afraid that it will cause my kids to lose their faith (atheists, your view of the world is just not that convincing):

Terry McDonald is chairman of the Metroplex Atheists. McDonald is thrilled that there’s finally a voice for his beliefs.
“The fear that they have seems to indicate a bit of insecurity about one book or one movie, and maybe that insecurity points to doubt about their own beliefs,” said McDonald.

It’s not insecurity or doubt, it’s the desire to respect God and not participate in mocking him. Sarah was filled with righteous indignation, not fear 🙂