Do I think The Golden Compass is Anti- reliious? No.
I believe that Pullman was simply expressing he views. I do not think he was targeting the christain population and trying to corrupt the minds of children. But there are many people who think that Pullman is a big threat.
One of the major concerns with the His Dark Materials trilogy is the perceived anti-religious content. The Church is portrayed as being completely devoid of morals and steeped in absolute evil. But, all of the negative traits of the Magisterium: greed, power, corruption, etc., are opposed by the positive ones associated with Dust. That is, love, free will, and knowledge. These also happen to be the traits that embody the God we know in the Christian religion.