Good point VA I did read The Golden Compass, and here is what I thought:
I did not really like the book. I do not think it is likely to become any sort of classic. I also do not think that I would have liked it if I had read it when I was a child. In fact, I think I would have been sickened by them as a child. It portrays a very bleak outlook on life, espcially for a "children's" book. For instance, several important child characters die miserable and undeserved deaths. I remember the first time I encounted a book as a kid that included real injustice as a part of its plot. It was hard for me as a kid to digest. Also the main adult characters turn out to pretty much pure evil.
Also it's climactic fight scence is quite graphic. Like, blood and severed body parts graphic. In a book for adults, this scence would be considered intense, but as a bedtime story for a child? Not if you want the kid to sleep again that week.
Its hard to say who this book realistically might be written for. It's really just too bleak and cruel for a children's book. And it requires you to take talking polar bears seriously, which makes it not fit very well into an adult or young adult type genre.
As to the anti-God stuff, I only read book one and it was not overtly anti-god. You can tell that the author has an athetistic worldview, but he doesn't get really preachy about it (unlike some other authors I could mention like... MERCEDES THE DORK LACKEY!!!!), which is a point is his favor.
And he does have some genuinely imaginative ideas.
But overall, the the author has a very serious shortcoming in that he has a seriously messed up idea of what appeals to kids.