I just finished the first book in the series. I did not read anything anti-God in it. The main religious sect that was portrayed in the book is supposed to be a Christian religion, I would assume Catholicism (not sure), does seem to be, at least a branch of it, pretty harsh. The idea the book is going with is that the humans of the fantasy world he has made up, have a Daemon that acts, from what I tell, almost like a spirit guide and represents the persons soul or part of it. There is also this thing called Dust that settles on a person when they hit puberty, and is referred to as "original sin". This religious sect has set out to cut the Daemon from children before they hit puberty. When they cut the daemon away most children die, some become zombie like creatures, and very very few live but are unemotional, almost robotic. The main character is a little girl who has control of a compass that tells the future, and she has set out on this journey to stop these people from killing children.
This piece is a pure work of fiction with its; daemons, armored bears, dust, cities that can be seen in the northern lights, and many other fantasy type things. Fiction is not reality. Any child that is brought up right will know that. If you want your child to be atheist raise them that way if the are strong in their beliefs a children's story is not going to change their mind and vise verse, if you want your child believing in God a simple story will not change their mind. Things are going to into your life that are going to challenge your beliefs no matter what they are, this is a good thing because it will make you a stronger person. It will make you study harder, ask more questions, and be knowledgeable about the world around them. I think this is what scares so many people. They do not want to question things and they do not want their children to question things. That is a sad way to look at life. This book did not change my belief and I really do not think it will change my five year old nephews belief, if I set down and read it to him. He is only going to care about the really cool armored bears.
Like I said I have just read the first book, therefore I cannot commit on the rest, but in my opinion the first book is cute. It is not as wonderful in my opinion as the Harry Potter books, or some of the Chronicles of Narnia (there were one or two that were kind of boring but I am an adult). I personally would go up against any religious or non religious sect that was doing harm to a child so if this child has to bring down this particular sect to stop it than so be it.
Another thing, Douglas Adams is, as far as I can tell by reading the Hitchhikers series, an atheist but no one made a fuss when that movie came out. I think they even have to read the first book in that series in school. I probably should not have said that. Some one reading this right now is having a fit. I love Adams' series. I highly recommend them.