The Christian Century has a cover article about The Golden Compass (the book -- they don't really cover the film) titled "The Enemy Church." The first book of the trilogy doesn't fully play out Pullman's theological challenge, so it's no surprise that any protest about the film was short-lived. I agree with Chris' comments below that Pullman's primary problem seems to be with original sin. It's a disagreement shared by a lot of people I know, even though many Christians would agree with GK Chesterton that sin is the one doctrine of Christianity for which there is empirical evidence. Pullman's characterization of the church as authoritarian and oppressive is no surprise either to most of us. We're accustomed to seeing the church as a pure caricature in the movies. And, quite honestly, we can agree with most atheists that historically the church has done a lot of Bad Things. Add to that the fact that Pullman's world is purportedly a fantasy world, a parallel universe of sorts in which the pope is John Calvin and people's souls walk about with them in animal form. If Pullman wants to criticize the historical church, have at it. Christians can at least agree that the church has often betrayed its own mission. If he wants to argue that we'd all be better people if we didn't believe in sin, well, there you have a matter to talk about, and I'm not sure the straw man of the Evil Church that he raises in His Dark Materials series helps advance that argument.