Philip Pullman is a self-avowed atheist. There was a big, silly brouhaha when the movie version of The Golden Compass came out, all kinds of people saying that Christians shouldn't go see it because it is anti-God. I doubt that more than a handful of people made it through the series to the last one and had any inkling about the true nature of the books. The first one just barely touches on religion; it's just a little bit anti Church but not really anti God. The second one is more anti Church but, again, doesn't say much about God. The third one, though, is very surely a rant against God. But you know the funny thing? It's very against God the Authority but it is very Quakerly in it's beliefs, anyway. This is from the last page of the book (**Warning-Spoiler**):
(Lyra is speaking with her daemon, Pan)
"I remember. He meant the Kingdom was over, the Kingdom of Heaven, it was all finished. We shouldn't live as if it mattered more than this life in this world, because where we are is always the most important place."
"He said we had to build something..."
"Thay's why we needed our full life, Pan. We would have gone with Will and Kirjava, wouldn't we?"
"Yes. Of course! And they would have come with us. But-"
"But then we wouldn't have been able to build it. No one could if they put themselves first. We have to be all those difficult things like cheerful and kind and curious and patient, and we've got to study and think and work hard, all of us, in all our different worlds, and then we'll build..."
Her hand were resting on his glossy fur. Somewhere in the garden a nightingale was singing, and a little breeze touched her hair and stirred the leaves overhead. All the different bells of the city chimed, once each, this one high, that one low, some close by, others farther off, one cracked and peevish, another grave and sonorous, but agreeing in all their different voices on what the time was, even if some of them got to it a little more slowly than others. In that other Oxford where she and Will had kissed good-bye, the bells would be chiming, too, and a nightingale would be singing, and a little breeze would be stirring the leaves in the Botanic Garden.
"And then what?" said her daemon sleepily. "Build what?"
"The Republic of Heaven, " said Lyra.
(Oh, I'm all verklempt again over the ending. It's so sad and sweet and hopeful.)
Many people seem to confuse The Authority with God. The Authority is The Church. God is Spirit, Life, Love, Truth. I understand the confusion. The Church speaks with authority saying it speaks for God, saying it knows the will of God. But it doesn't. The Church speaks for it's own power. God speaks quietly to the hearts of us all, letting us listen and hear in our own time, when we are ready. God is best represented in these books as the daemons which each character has, the spirit of each person. The Authority is no more God than mulefa can fly.