I think a large part of it is simply the pedigree of these franchises. For decades, Batman and Superman practically carried DC Comics' brand in film at Warner Bros., and, for the first time in 70 years, these characters are finally meeting on the big screen, and it may not even pass the $1 billion mark. You combine that factor with the extravagant budget WB assigned to this project, and, as much as I love the film, it's not difficult to see how it could have shaken people up a bit. Ultimately, though, I think WB has the right idea with the "bigger picture." I feel like, at the end of the day, this film succeeded in what WB wanted it to do; it kind of salvaged Man of Steel, and it set up Justice League, but it did so in a bizarre way that left a lot of people very disappointed.
Gradually, I think we might see improvement. It's all about finding balance, and I feel like Snyder is still trying to figure out that perfect formula. Batman V Superman tried to accomplish a ton of stuff, and I'll give them credit for that until the day I die (probably not, as, ideally, by that point I won't be able to remember my kids' names, let alone that movie I saw 50 years ago). You put the two most iconic super heroes on screen together, you, basically, set up Justice League in one film (albeit in a bit of a heavy handed manner), you had this weird, avant garde drama with all this subtext that, may have soured a lot of people who just wanted to see Batman punch Superman in the nards, you basically succeeded in kind of adapting the Death of Superman.
I mean, ****, for all its faults, you can't say Snyder and co. didn't lay all their cards on the table in a really unique way.