Controversial topics can make some of the most memorable and brilliant novels, when handled correctly. However, I find that no novel is going to change someone's predispositions, and therefore angry readers will abound.
I've mentioned this more than once on these boards, but I loved Lolita. I think it's brilliant. One day, I was reading in the library. I hardly had surpassed page two when the librarian came up to me, looked me straight in the eye, and said, "That is a truly evil book." I must have goggled at her for two minutes until a friend, who had finished the book and enjoyed it, started up a debate with the librarian. The librarian ending up leaving, saying something about how we would understand the book more "once you have children of your own."
It's my opinion -- and this isn't necessarily true for all readers and controversies, but many of them -- that the readers aren't fully understanding the point of the controversy in the novel. For example, Mark Twain was dreadfully misunderstood when he wrote Huck Finn. School districts are constantly under battle because of the use of a certain word in the novel, which Twain used to make a satirical point on society. When I was reading the book as a part of my school curriculum, we also watched short documentaries filmed in districts where Huck Finn was banned. It was obvious that many of the parents on film displaying their distaste for the book had never read it. They simply knew this word was used, not how or why, and wanted it removed.
If the opponents don't realize, or perhaps just don't understand the novel's tone, this is when I believe things get out of hand. Something like the Da Vinci Code, on the other hand, which constantly pushes at the Catholic Church, does have a legitimate hype because some of the book's theories come from scholarly background.
As for "hate mail," there's really nothing much to do other than ignore it. Unless the novel becomes truly popular like the Harry Potter series or the Da Vinci Code, the hate scandals won't get any press. Both sides of the controversy are addressed in these cases because the public are interested in it as entertainment value. No one sitting at their dinner table listening to the evening news will suddenly halt eating and proclaim, "My god, J.K. Rowling is demoralizing children across the globe!" or "Dan Brown has finally uprooted all the evil of the Catholic Church!" unless they already believe it to be true. It's not until the book catches press, either, that the controversy will matter in book sales. People will want to read it for themselves if it's in the news, but by then the novel would have already sold a good chunk of copies.