The Independent has Q & A session with Philip Pullman. Among the questions was this one:
You famously criticised CS Lewis for incorporating Christian values into his books for children, and yet you do the same with atheism in your books. Isn't this a double standard?
Atheist values in His Dark Materials? Well, I guess it all depends on what you call Atheism. While God, angels and fallen angels all unquestionably exist in the books, the values are overwhelmingly humanist; it's all about us. Whether you think that this is atheism will obviously depend on which particular brand of Christianity you subscribe to, but there's no necessary incompatibility between the two, as any C14th Italian will attest.