Not because he's an atheist, but because he completely misreads Tolkien: "No-one is in any doubt about what's good or bad; everyone knows where the good is, and what to do about the bad. Enormous as it is, TLOTR is consequently trivial."
Lots of really interesting stuff in the interview, which is on one of my favourite blogsites.
And for the record, I really enjoyed 'His Dark Materials', I'd be quite happy for my children to read them in due course, and I have a quotation from Pullman stuck on the side of my computer box so that I can ponder it every day. I just think he's got rather a significant blind spot.