I think it was a combination of 1) it was a Watchmen-style deconstruction (Snyder explicitly said he was doing just that--i.e., applying the same project of Watchmen to Superman and Batman--in a WSJ interview that was published on opening weekend)... which I suspect many critics didn't even grasp... and 2) Lex Luthor is just so weird, creepy, and offbeat... that the result was something too non-traditional for many to tolerate.
The pure shock of what this film does artistically and at philosophical meta-levels I think get translated into "poor execution," "Snyder doesn't get what makes the character's tick," and "Snyder is a terrible storyteller who sucks at narrative structure," etc. There is typically no explanation, no shift in approach to understanding or appreciating the movie, that will satisfy people that see it that way. Imo they chafe against what this film did at its core even if they sometimes say they could have tolerated the same themes and aims of the story by some other director who if given the chance would "execute" it better.
I've had conversations with those that dislike the film where I have compared certain aspects of BvS's narrative structure and overall tone or mood to 2001: A Space Odyssey and Blade Runner and they completely deny that there was anything whatsoever challenging for the average GA viewer to those films regarding narrative structure and often how little exposition there was, i.e., where the viewer has to work a bit, and maybe require several viewings, in order to make sense of meanings that on first viewing may not be easy to follow. It's just outright denial.
BvS is going to continue to grow it's cult following over time, I am confident of that.