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.
my 1st thought as well, but as grrlfman2 says above, it's the texts of (books 2 + 3) in his trilogy that are controversial. Having custs complain about stock because they personally have issues with that title, that section, is a perennial, though.
Yeah i figured that too, but that could be because i recently had to pay out on a SMOF who was bagging OSC for his views and much like the strip i countered with: "So what? Its not like Ender's Game is how to be a fundy Mormon." (The discussion was considerably longer and more detailed than that but the gist was the same.)
They remind me of the Bunny Suicide and Happy Bunny books, but that's just because they tend to mention bunnies and I've recently read/looked at my Bunny Suicide and Happy Bunny books. No clue what they're actually about, but I'm sure enjoying them!