It's the same reason they hated the recent Judge Dredd movie as well. This Joker movie has really illuminated something. These people are still children. They truly dont have a concept of what evil actually looks like in the real world. It's never some dark lord who goes about in a black Cape looking all evil and being bad because he wants to be bad. Evil can be some mentally ill loner who cares for his mother and gets kicked one too many times. Or in the case of Dredd, a beaten up former whore who has had a few screws knocked loose and doing what she thinks she has to do to survive in a society that has to eat it's own dead to function.
They simply cannot deal with Evil that is not only plausible but known to be real. And they certainly cannot deal with the confrontation of what actual violence is. Hell even the Berkley riots were just a bunch of Kids Larping at being revolutionaries. Not one of those black clad morons were actually setting out to kill someone. The more recent incident with the bike lock dude, even he probably was not actually thinking he was going to kill the dude he brained with it.
And such an uncompromising depiction of what evil actually is and what violence actually is makes them realize that if they encountered the Joker on a subway train at 1 AM, they would not be the bat man. They would just be a simple salaryman who incidentally, also does not have a gun either, or the will to use it.
And that is absolutely terrifying.
Evil rarely ever stares you down in the face. Not to mention that evil is a reflection of good and hard to tell apart. Janus, Ying-Yang and other theological questions have always dealt with this.
The best villains are villains that would be heroes or are nearly indistinguishable from them. Because that's what evil IS. People laugh at Dick Cheney and call him evil, but he's a man who loves his children, his family. Its incredibly complicated and everyone wants evil to be boiled down to some sneering dude twisting his mustaches. Why do you think they use the much copied 'Trump is Voldermort'? Because they cannot truly understand the depths of what evil actually is. The man, for all accounts, loves and cares for his family. Has many friends. The problem is his political views don't align with your own.
Once you begin talking about the 'greater good', you've lost sight of it. Because if you believe in the greater good, you are disregarding other people for a goal you see as good. You are purposefully ignoring their pain, their families, their problems, in order to solve something bigger. You've become a callous individual and are hoping that the change you make overwrites the sins you are going to commit in furtherance of that goal. I'll tell you right now, it never does. Because once you bloody your hands, that never comes off. And you have to continue to sin, continue to use people. Continue to hurt them, for your goal. And eventually, you don't see other people as people. You see them obstacles to your goal. There's no way you can see yourself objectively anymore.
These people can't take a step back and watch themselves. They believe because they believe in 'righteous' causes, their actions by default cannot be evil. Because evil is always obvious, right? And its not speech. Its actions. Its brigading some guy on Twitter because he made a joke you didn't like, trying to make him lose his job. Its making allegations decades after the fact because you convinced yourself they were true. Its throwing molotov cocktails, destroying property. Its hurting people in the name of your message, because your message is just, and these are all pawns. They don't have emotions. Cares. Feelings. Families. People they love. Dreams. They're nothing. They're alt-right. They're incels. Fuck them. They don't deserve it. We are the right ones.
Once you begin to dehumanize people, view them as objects, demons, devils or not even as people anymore, you are stepping down a road you will never be able to come back from.