I've had to explain that too. I think the problem is that after watching the Star Wars prequels people assumed that the makers of BB were trying to do something similar (that is, base the whole movie on links to the old ones). Superman Returns probably enforced that notion, too.

It's obviously gonna be confusing to the general public to see a movie where Bats meets the Joker for the first time, if they already saw that in the 1989 movie. But fuck 'em, I say. They're only gonna let that annoy them if they want to.