You should read Hanna Rosin's piece on the making of the movie, and her review of the finished product; you can find my own (none-too-favorable) review in the next National Review. But to understand what went wrong with Chris Weitz' adaptation, look no further than this:
Mr. Weitz says that if he gets to film the rest of the trilogy, he will begin right where the current movie leaves off. “I mean to protect the integrity of those remaining chapters,” he explained. “The aim is to put in the elements we need to make this movie a hit, so that we can be much less compromising in how the second and third books are shot.”
Translation: "I know I made a mediocre movie, but hopefully people will go see it anyway and the studio will give me a chance to make the sequels the way I want to make them." Sadly, with a $26 million opening weekend, The Golden Compass has a long way to go to make that bet pay off. (And Compass was the best of the books anyway ...)
More in this vein here.