So what we all know about Pullman is that he is an atheist. The mere word strikes within many of us a negative connotation, going against our childhood teachings of God's love and Jesus' sacrifice. He demonstrates that he knows the bible well, almost parodying it in his trilogy, and yet he rejects its ideas and stories. Yet he denies that his book reflects these views? Hmmm...
One might argue that Pullman's book is absolutely evil. I mean really, he kills God. In a children's book. He portrays God and organized religion as child-killing, mind -controlling fiends. His main Character Lyra is a little con artist who survives by telling lies. What kind of book is this?
On the other hand, Pullman's book encourages critical thinking by challenging authority. Lyra displays love and loyalty to those close to her. She learns her lesson about lying when the harpies call her out. Lyra basically saves the world and banishes evil, so how could she be bad?
I think that what Pullman's book does is demonstrate that there are flaws in each of us. Many times literature portrays a character as wholly "good" or "bad". Literature is meant to teach lessons or morals, and many times these morals are black and white, which is not the case in the real world. I think what Pullman encourages is understanding, which is one of the most important lessons you could learn.