See this Snopes.com article on Phillip Pullman's
The Golden CompassI don't think the His Dark Materials series made a good case for atheism in the first place. I didn't know Phillip Pullman intended to pit himself against C.S. Lewis but while I read the books they did make me start comparing with the Chronicles of Narnia. I was dissapointed. The characters were as rich, the worlds were as imaginative, but in the end His Dark Materials simply did not resonate. Whereas Lewis' tales touched me to the quick with profound truths, Pullman's were clever but in the end left more questions than answers. Lewis tells you how the world was created, how evil came into it, how the Creator defeated the evil, and what is to come. Pullman tells you that "religion" is oppressive and cruel, and that God is a sham. If Pullman was trying provide an atheistic counterweight to Lewis' Christian worldview he did not do a good job. Here are my reasons for thinking so:
1. The religion he criticises isn't a true reflection of religion in the first place, it's his own take on religion. He set up a straw man to attack.
2. The universe he depicts seems more pantheistic than atheistic. Everything is made from "dark material", particles that are somehow conscious, and when they die they dissipate into these particles again. There is a belief system in operation. In the story there is a atheistic scientist who was formerly a Christian, however as the story unfolds she comes to accept the pantheistic worldview because she starts to interact with the dark material and learn its nature.
3. The whole story is about the battle of good against evil. If a pantheistic or atheistic worldview is being promoted, where does this concept of good and bad come from?
My personal take-away from comparing Pullman with Lewis is that an atheist cannot write children's fiction. This is not a facetious observation. Three characteristics of children's stories are that 1) they are moralistic; 2) they are imaginative, i.e. creative; and 3) their purpose is for edification in some way or other. Where does an atheist draw right and wrong from? Don't atheists deal in proven facts rather than whimsy and fantasy? What words of encouragement would a true atheist have for others that does not mean imposing his own personal "truths" on them? No, there is no atheistic children's story because children with untainted minds are nearer to the Kingdom of God and cynical atheistic thoughts wouldn't appeal to them. While Pullman's intention to introduce atheism to children is reprehensible, it is ironic that in writing something that has to appeal to children he is forced to abide by the three characteristics of children's stories and thereby forced into a realm where atheists cannot survive.
By the way, C.S. Lewis was himself an atheist who came to the conclusion that atheism did not fly. He then contemplated pantheism and Christianity, and in the end became a Christian.