It's not Philip Pullman, it's living in a Christian society. The Enlightenment growing out of the Reformation meant that all the foundational atheist thinkers had deeply sentimental views of Christianity, which is how you get the Jefferson Bible (yes, a deist), and that Pullman quote and many more like it. "Well if you strip away all the things I don't like, this philosophy is very compelling" is only a conclusion you could come to when you already are predisposed to like the philosophy.