For me, White's Trumpet of the Swan is his best book. I know most people love Stuart Little but he wasn't really a mouse. As for Charlotte's Web, I was never that good at spelling.
I would like to imagine that Web is banned because of the spiders and talking bacon. I can understand if Farmer Joe gets upset because his children don't want to kill the pork money. But that's not the reason, at least not really.
It's death. Death hangs over this book. Charlotte dies at the end, and Wilbur, for a good portion of it, is in danger of being killed. But most children when they read this book have already encountered death. White gives kids a way to deal with it.
Unless, it's the idea of talking animals being the agents of Satan.