To try to put this as simply as possible:
His Dark Materials is not anti-Catholic in the sense of being against people who are Catholic, but it's kind of obviously against the Catholic Church in specific and institutionalized and/or politicized religion in general. It is also a series of books whose key event SPOILER ALERT is two twelve year olds doin' it while in the midst of a quest to kill God for the betterment of the world.
Philip Pullman, the author is very public about his atheism and his distaste for organized religion. Or at least, he in is his native England, where saying such things won't get you persecuted as a public intellectual and children's book author. Meanwhile, William Donahue of the Catholic League is a religious extremist nutjob who has dedicated his life to undoing the Establishment Clause of the Constitution and to saying things like "Hollywood likes anal sex. They like to see the public square without nativity scenes. I like families. I like children. They like abortions. I believe in traditional values and restraint. They believe in libertinism." while sticking up for Mel Gibson's The Passion of the Christ (described most colorfully by Christiopher Hitchens as a "pogrom of a film"). Donahue also tried to stop the NY State Legislature from requiring the Church to report allegations of sex abuse to the authorites. He also lead a crusade against two progressive bloggers who were hired by the Edwards campaign, a crusade that ended in the resignation of the two bloggers amidst multiple threats of rape and murder.
So the real question is... Why the hell is a clown like Donahue able to get airtime to talk this bullshit? And, secondarily... if moderate muslims are supposed to stand up and condemn extremists in the faith, are Catholics required to speak out against pharisees like Donahue?