I guess it's hard for me to separate Pullman's statements on the matter from the material in the book itself. I believe him when he says what his intentions were. Perhaps if I had read the books prior to hearing what he said they were about I would feel differently.
Similarly, I thought the DaVinci code was a decent romp when I first read it. Then I heard/saw Dan Brown out there trying to convince people it was all true. That ruined his books for me.
Yeah, the books don't say there is no God, just that the angel currently claiming to be God is lying. He was the first angel created, so when all the other angels came into being just after him, he kicked back and said, "See what a good job I did, guys?"
But that angel is the God of all of the religions in the book, right? The gap is pretty narrow between that and Pullman preaching that the God that all reallife religions and religious people worship (like myself, for example) is not actually a God, but a charlatan who deserves to be put down and overthrown. And I know a lot of people who love the books cherish that element of it.
It's sort of like me saying that I made up this story about these two friends on a Star Wars message board (not this one, it's fictional) named Bingowings and ChainsawAsh (not you two, these are just characters in my story) and they are the ugliest fellows you ever saw. You might feel a little offended at that, no matter how many times I assured you it was all a little fiction I came up with, right?
But like I said, perhaps I would see it differently had I read the books without the influence of Pullman's extratextual commentary.