I found a piece in the New York Times that Nathan referenced about why the film version of The Golden Compass ends three chapters before the book (no huge spoiler, but read at your risk):
Fans of Mr. Pullman’s version may be surprised to learn that the movie stops before the book does, leaving out Lyra’s long-anticipated meeting with her father, who plans to wage war on the Almighty himself. Instead the movie ends in stirring fashion, with Lyra saving the kidnapped kids from what amounts to spiritual lobotomy and heading off in an airship with Iorek, an armored bear who has become her friend and protector. There was tremendous marketing pressure for that, Mr. Weitz said. Everyone really wanted an upbeat ending.
He added, They’re looking for a franchise here, meaning that if The Golden Compass does well, the studio will go ahead with films based on the two remaining volumes of the trilogy.
The foreshortened end of The Golden Compass also has the advantage of lopping off some of the book’s most heavy-duty theological discussion (presumably leaving some of the thornier issues to the sequels).
[…]
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.
None of this is a huge deal, obviously, it was just surprising to me when the credits rolled because I was looking forward to the pretty colors in the big Aurora scene. New Line’s The Fellowship of the Ring and The Two Towers both also ended at different points than the books.