I don't see that many people, if any at all, claiming that those who didn't like the movie didn't get it. Not that there aren't people like that, but this idea that us, who enjoyed the movie, claim you didn't because you aren't smart enough to understand it is just ridiculous. I never said anything like that and i usually don't see people saying it either.
I do, however, believe that some movies might just not have the right elements to please the masses at a certain point in time. Not every artistic work is for everybody. This is just a fact. You still have a big percentage of people who loved the movie. Are they stupid? Dumb? Or are they simply able to enjoy a certain type of movie that rubs a lot of other people the wrong way?
It's not that people don't understand the movie. The problem with this movie, aside from being flawed on several levels, which isn't unusual in a superhero film, even in those that receive decent reviews, is that it had unreal expectations around it. Around the story, the characteristics of the characters, the visuals, etc. Expectations that movies like Ant-Man or Thor never had, because most people don't know enough, or care enough about Thor to nitpick the hell out of it and complain about the character not being exactly the version they hoped for.
Batman and Superman are always going to be more controversial than any other character. Doesn't mean you can't make a crowd pleaser with these characters. But i honestly believe it's going to be a lot tougher than with any other characters. The movie isn't perfect. But it isn't the piece of garbage that some people claim.