The current anti-Pagan theme seems closer to deal with the bizarre fear that certain Christians have. There is a brand of Christianity that is based on fear. That's how they recruit - "If you die tonight, you might go to hell if you don't accept Jesus right now!!" They attack Harry Potter, ironically, and claim that he recruits Children to WITCHCRAFT! AHHH.
Ironically, because HP, in my opinion, is closer to a Christian alagory. HP is a nobody, and his relatives hate him. His relatives (the world, or "muggles") represent gluttony, self exhaltation, gossip - basically, the 3 of the 7 Deadly Sins.
HP then is shown a secret world (the spirit world) where he is actually a bit of a hero (Christians are told that they are all royalty and Princesses and Princes to God.) There, he meets those who use their power for good, and those who use it for bad. Harry must often choose between good and evil. Dumbledore plays a kind of Omnipresent God that gently guides, but allows Harry to learn on his own. He intercedes if Harry is in real danger, but Harry confronts Voldemort (evil, the devil), and while the defeat is temporary (you can't really kill evil), with each defeat, Harry grows magically (spiritually.) It also teaches the importance of friendship, humility, being honest with one another, choosing what is right .... frightening! Come quickly Lord Jesus, AND SOOOON!
I think there is also something deep down (doubt maybe?) when this same brand of Christianity is challenged by someone who is perfectly comfortable and happy not being Christian. The very idea is foreign to them. Many, many times I have had people tell me that I'm not happy, or that I simply am unhappy but don't know it, and the only way that I will ever know true peace and happiness is through Jesus. Ever meet a Buddhist monk? That is far more peaceful than say, Jerry Falwell or Pat Robertson.
To see someone simply happily living a different life can be threatening to the very core of someone that insists that there is only one way to live.
I also think that some of it has to do with ignorance. There is a bizarre understanding that Pagan = Satan worship. Some will argue that anything not directly of God IS Satan worship, but to me, Paganism is actually not so distant from Christianity. There is the standard Do Unto Others (Do what you will and harm no one). Pagans cast spells asking for blessings. Christians simply pray for the thing they want. Again, very similar idea. Praying to win a basketball game is extremely close to trying to cast a spell on the other team in order to win.
I suppose that the more people learn, the more this kiknd of persecution will die off.