I read The Golden Compass several years ago and enjoyed it but apparently didn't feel compelled to read the rest of the trilogy at that time. With all the emails exhorting Christians to boycott the new movie because of the anti-God agenda of the books, and considering that my 11-year-old has read the trilogy, it seemed like a good idea to found out for myself what the message of the books is.
Verdict: definitely anti-religion. Having said that, as is common to things anti-religion, the big, bad religion described in the books, while it may resemble the Catholic Church of hundreds of years ago, doesn't really reflect any modern Christian religion that I am personally familiar with, though a teenager on the brink of rebellion might think differently. The overall message of the book is that tolerance, the search for knowledge, and the appreciation of beauty are good, while narrow-mindedness, prejudice and killing people because they threaten your goals of world domination are bad. I don't have much of a problem with that, but it's less appealing when equated with religion vs. ... what? Non-religion?
It's also just less appealing in these books because I didn't much like them. The story was complex and somewhat suspenseful, and there are certainly some interesting ideas introduced (though not fully realized), but many of the characters are amoral, not very sympathetic, and oddly motivated, and there's not one shred of humor in any of the books. I didn't notice how much this bothered me until I read Good Omens, by Neil Gaiman and Terry Pratchett, while I was in the middle of The Amber Spyglass. Good Omens, while also dealing with an epic battle between good and evil heralding the end of the world, was hilarious, and thereafter I struggled to finish the other.
The third book is particularly cumbersome, with extra (and weird) characters being introduced for unclear purposes, the main characters going on strange and inadequately explained quests, and just lots and lots of stuff to slog through. Like I said, it was a struggle to finish it.
My 11-year-old, when questioned, seemed unaware of the anti-God message in the books, but an older, more analytical teenager might see it. I think it might be interesting to read these books together with my kids and talk through the generalizations and problems, but only if I enjoyed them more.
If you're interested, you can look at one review of this trilogy on Amazon that I thought was particularly good.