That's actually incorrect, there was a timeline where the joker left Gotham to go tamper with metropolis. He had a scheme set-up that destroyed almost the entire city AND the unborn child of superman; that's a comic where superman and louis were together and tried having kids.
Superman then proceeded to become a dictator for the earth, encasing all the villains in high security prison and flaunting his power over other heroes and humans for the sake of the safety of mankind, with wonder woman at his side. Getting into the nitty-gritty would take too long of a type but, Batman and a few of other heroes who rebelled from his command overthrew Superman or atleast snapped him back to reality. To atone for his sudden take over He was placed in a red-sun prison off planet
Most of the stories with the heroes having flaws are usually when someone decides to take it too far, so really and truly it's more so narrative and perspective on what you want to see. Like when Batman finally started Killing, and so on...
