Apparently (according to Bill Donohue on Friday evening) the organizations of Atheists in USA and England love Pullman's books and were very disappointed that Hollywood "watered down" the militant anti-Catholicism in the movie.
Donohue's suspicion has been that the real issue is that like other "movie franchises" they were looking for 3 movies, reflecting the 3 books in the triology, plus, and more importantly, tie-ins to the books (a la Lord of the Rings) and merchandising revenues. That will depend on the success of this movie.
Apparently, the books themselves are a) aimed at teenage fantasy readers, and b) militantly atheistic, antireligious, and particularly, anti-Catholic. The Catholic League's take for months now has been that Pullman and the Atheists are hoping for big sales of the books as the payoff to their ideology. Pullman's Atheism & AntiCatholicism
The above link contains many quotes directly from Pullman, where he shows the tenor of his anti-religiosity. (Click on the PDF pamphlet icon on the left of the main page, and then on the link that shows up.)