While the recent controversy over his books may have seeded the idea, I don't think these are explcitly about his books. After all, the "offensive" ideas from Pullman is what's in his work, not something in his real life (that I know of, I don't actually know anything about Pullman the man).
Pullman himself is an atheist, nor is he shy about it. I expect that he'd get much less grief over his books if he were, say, a devout Anglican. He says that the books are about questioning; some religious folks think they're anti-God/religion/Christianity.