I'm a little late to the party on this, but I thought I'd throw my $.02 in...
I've read all of Pullman's work, and the HDM trilogy is one of the best collections of fiction I've run across in a while. Kind of like Harry Potter, except good.

Yeah, I'm a hater. What can I say.
Actually, I think the HDM trilogy is such a welcome departure not only from Rowling-esque juvenille fiction, but from the type of fantasy novels that have been gaining (or more often RE-gaining) popularity over the last 10 years. For once, someone writing a book that is expressly for younger people has the cajones to say, "Hey kids, religion isn't all good...in fact, it's not even
mostly good." Don't get me wrong: I love LotR and Narnia as much as the next fantasy geek, but Pullman's books not only manage to take a view of Christianity that is pointedly opposed to Lewis' and Tolkien's, but do so while still writing fantastic fiction and not just a heavy-handed atheist manifesto masquerading as a kid's book.
But my focus here isn't to debate Pullman's motives in writing what he wrote, but to talk about what a wretched, almost incomprehensibly awful job the filmmakers behind The Golden Compass did. Someone check real quick...Nicole Kidman has an Oscar, right? And the director of this travesty still got a mediocre (at best) performance from her? Congratulations, dude...you've earned a career directing USA-network specials. And the casting director definitely got the wrong Dakota for this role. Dakota Fanning would've been so perfect for the role that she might've been able to at least partially bail out this titanic flop, but alas, we get Dakota Who..er..I mean Blue, and a Lyra that could've been played more convincingly by most 10-yr-olds in your local community theater.
As a previous poster has said, you can't expect there not to be some significant story elements left out when adapting a book for the screen. Tom Bombadil was completely left out of Fellowship of the Ring, but Jackson still managed to make up for it with an amazing film. But (and I'm trying not to exagerrate), the storyline in this movie made it seem at times as though the screenwriter hadn't even read the book, or if s/he did, read it the night before filming began. A short list of ridiculous changes/omissions includes:
--Mrs. Coulter's hair is the wrong color. Pullman goes into some length about the qualities of her brunette hair.
--No background whatsoever is given as to why Lyra occassionally quarrels with gypsy children
--There are several aleithiometers left in existence at the start of The Golden Compass, but in the movie they say the Lyra's is the last one. If they intend on making the other 2 movies, this is going to cause some more story problems.
--The Master of Oxford college poisons the Tokaii, not the Friar. There was no reason at all to make this differnt in the movie...again, showing that perhaps the book wasn't even read thoroughly.
--The scene where the severed daemons are freed is left out, and then one of the gyptian mothers talks of "finding" the daemons.
--Peter dies in the book shortly after he's found by Lyra and the bear. In the movie, he lives and has a tearful reunion with his mother. Why? This contributes absolutely nothing to the story.
--Perhaps worst of all, they DON'T KILL ROGER at the end. This is enormously important to the overall story, and they just flat gloss over it. The movie ends with Roger and Lyra flying off together to save the day.
As the for religion theme, it is crucial to the story. No, the movie could not have been (was thus wasn't) made well by not giving due attention to the fact that the main story of the whole trilogy is
the quest to kill God. It's not as though the books make a couple of fleeting jabs at established religion. Pullman had a definite aim with these books, and afer Hollywood watered down the main theme of the books beyond recognition, we're left with what amounts to a bland, mediocre, poorly acted Narnia-esque snoozefest.
Really, I love Pullman's books so much that it actually angered me to sit through this crime against humanity masquerading as a film. How many people will be turned off to Pullman's books now that their first impression of his work is this awful, awful movie. I sincerely hope that if plans are in the works to make the other two books into movies as well that they A.) fire the director, screenwriter, and casting director, and B.) completely remake The Golden Compass. Seriously. I think they should just issue a public apology for their first attempt, and actually go back and make the film right the second time.
There are dozens of other terrible (but totally true) things I could say, but I think you get the picture. If you have the financial means to do so, upon the DVD release of this movie, buy every copy from your local retailers and burn them. Being in theaters is bad enough, but distributing this movie for purchase en masse is tantamount to introducing plague rats into the heart of New York.