Gotham city isn't really controlled by anyone in particular. But, is there someone who indirectly controls Gotham City? Through his actions batman controls the way people act within the city and this controls the flow of the city. He dictates what the joker will do. The joker is the character who controls the chaos but Batman controls the Joker. Many people believe that the Joker has full control over Batman, but if Batman wasn't around, the Joker wouldn't be either. The relationship between the Joker and Batman indirectly controls the entire city of Gotham.
People frighten the Joker within Gotham City. Although some people do not trust Batman, he is one of the only people willing to try and stop the Joker. Because of this, he controls many of the thoughts that go through the citizens minds. If the Batman has the ability to control the thought process of most, doesn't he technically control them? Batman also controls who is targeting by the Joker in the city. Since the Joker wants to attack anyone who gets close to Batman, Batman is indirectly hurting these people. So, not until all evil is ridden from Gotham City, will Batman stop controlling it.
