Here's the good news: The Golden Compass does not promote atheism. It isn't going to steal your children. It does not signal the end of hope for religion in the West. That's the good news. Here's the bad news: it promotes the same, shallow "don't touch my stuff or I'll kill you" message that appears in so much of popular culture. But more than this, in spite of delightful visual imagery, and a couple of performances in which it's clear the actors are having fun (an icy Nicole Kidman, and the great English theatrical knight Derek Jacobi to name two), it's simply a boring film.
At its centre there is at least an attempt at exploring interesting territory – we are in a parallel universe in which everyone is accompanied by a 'daemon' – an animal representation of their personality, and a comfort in times of trouble. Meanwhile, a shadowy authoritarian body, "the Magisterium", is abducting children and performing daemon amputations. Too much daemon, too much free will, too little for the Magisterium to do.
The religious resonances are obvious, but the film doesn't make any explicit commentary on Christianity. Rather, its enemy is the misuse of power to force people to think or act against the exercise of freedom.