"Our fear is the parents who don't know what's actually in these books and don't learn about it from the film may think [the books] are great stocking stuffers for their kids on Christmas morning," Kiera McCaffrey, the spokeswoman for the Catholic League, told ABC News.
"Every single religious character is a terror in these books," said McCaffrey. "There isn't one who isn't. And the heroes of the book — the children — are taught that churches are all the same and that they obliterate good feelings."
McCaffrey said that the Catholic League has distributed thousands of copies of pamphlets about the film in hopes of discouraging people from seeing "Compass" and is also telling people to boycott the film and books.
"This isn't just a book that promotes atheism," said McCaffrey. "It denigrates faith — particularly Christianity. If there was a trilogy of books that were racist or anti-Semitic we wouldn't say 'lighten up' or 'let's let kids see another viewpoint.'"
But the importance of seeing another viewpoint is exactly what the Catholic League fails to understand, according to Annie Laurie Gaylor, co-president of the Freedom From Religion Foundation.
"It's time we get past superstition, embrace reason and put our energies in the real world and not in a fantastic afterlife that nobody can prove," Gaylor said. "Why shouldn't our society be open to other views?"
Several film critics told ABC News that any film that hints at religion is likely to provoke a debate, much like the one surrounding "Compass."
"Whether it's controversy about religion or sex or violence, we look at them and there are certain hot-button issues that if they get addressed are bound to be controversial," said Jed Dannenbaum, a film professor at the University of Southern California. "[Pullman] identified himself as an atheist and I imagine if he'd never said anything nobody would have particularly noticed that about the books or the film."
"Something that challenges the prevailing religion in the country will always be controversial," said Dannenbaum, who added that he'd be more concerned about parents monitoring their children's exposure to violence than movies like "Compass."
More worrisome to religion and film experts was the way in which some people would rather silence conversation about complicated issues, rather than encourage it.
"'Harry Potter' didn't make a bunch of atheists," said Diane Apostolos-Cappadona, a professor of religious art and culture history at Georgetown University. "Discussion of religion has become so painted and so questionable that I don't think we're sitting down and asking the fundamental questions."
"I think these movies begin conversations," added Apostolos-Cappadona. "What is more harmful than shutting out conversation and ideas?"