The Golden Compass is sneaking science fiction into the holiday movie season, which is usually reserved for magical wonders and barely-funny revamps of the Santa Claus myth. The movie may be wrapped in fantasy trappings with its brave-but-cute kids and talking bears, but The Golden Compass will be more steampunk than Narnia. In fact, the studios are misleading audiences by characterizing this hard-edged flick as fantasy.
OK, so there are witches, but most of the coolness in The Golden Compass comes from fantastical scientific machines rather than pure fantasy. Even the golden compass is a machine that Lyra just happens to be miraculously adept at reading. The whole story is set in a parallel universe, with its own set of scientific laws, which is a story setup well-known in the annals of science fiction. Parallel Earths are de rigeur in time travel stories as well as scifi TV like Sliders.
So the talking bears and other creatures aren't magical, but simply a variation on how life might have evolved on Earth. Maybe the daemons (the animal familiars that everyone has in Lyra's dimension) seem magical to you, but at least in the books they are portrayed as a part of each person's anatomy. They are essentially organs, parts of each person's brain that exist outside their bodies. They are not "souls." And the mythical "Dust" that Lyra's dad is trying to track down isn't magical either. It's a controllable particle that helps make up the fabric of the universe.
Maybe the reason why Christians have been protesting the movie is that they don't like seeing science seep into a story that also tries to deal with ethics and religion. And make no mistake, there is religion in this flick. It's just that the so-called gods and angels are more like the powerful alien New Gods and superheroes from comic books — they aren't magic, just have cooler powers and better technology than the humans and other creatures. Offering a scientific explanation for religion, even if it's a scientific explanation right out of pseudo-science TV show Heroes, may be the sneakiest trick of all for this stealth steampunk classic.