Throughout the history of comic books, people have always rooted for the morally good heroes who are justified in the way they protect people and stop evil people from hurting others. I know that whenever I read a comic book or watch a comic book-based TV show or movie I am always inspired by the people who are so selfless that they will sacrifice their very own lives in order to protect innocent people. These heroes always do heroic actions for the right reasons and not for themselves, but this does not mean we are not drawn by a deeper and darker version of dishing out justice to those who deserve it.
This kind of justice is dished out by the group of characters that are known as anti-heroes. These people are referred to as anti-heroes because they are doing their best to stop evil people, but they do it in not so morally justified ways or even only for themselves and helping others is just a natural side effect of their work.
My personal favorite anti-hero is The Punisher from Marvel. I always find myself rooting for Frank Castle even though most of the time his actions are not those of what most people would call a hero, but to many people, these characters could be called heroes in a dark way.
Frank Castle was an elite special forces operative with the United States military and served his country to the highest degree. He retired from the service in order to pursue a quiet and normal life with his wife and children. This dream of his, however, was destroyed though when his entire family was murdered in cold blood in front of his very eyes by New York criminals ranging from the Irish mob to a biker gang. Frank was shot in the head and almost died but made a full recovery physically but his mental and emotional health were all but shattered. Hell bent on revenge for his family, Castle sets out on a mission to "punish" everyone that was responsible for his wife and children's murders.
Now Castle does not just catch the bad guys and sends them to prison. He delivers his own brand of justice to these evil people that results in them being buried in the ground somewhere sending a message to all of the other violent criminals out there. If you hurt an innocent person and The Punisher finds out, you better watch your back or you'll be finding a bullet in the back of your head.
I believe that people find themselves rooting for the Punisher even though he willfully goes about taking the lives of other people is that we identify with his motivation as a character. He witnessed the people who he loved the most in his life being taken him forever for no reason at all besides the motivations of some greedy criminals. Castle's reactions to this tragedy are very raw and human. I believe it would be a desire for any person that witnessed their loved ones being murdered in front of them to see those responsible pay for what they had done. Humans can be very violent creatures and I think that is why many people root for The Punisher to succeed in his mission.
We are tired of seeing evil people getting away with horrible deeds just because they have a lot of money and are able to buy their way out of serving the consequences of their crimes. We as readers enjoy seeing The Punisher dish out the pain that these evil people enjoy inflicting on innocent people for no reason besides their greed or sick pleasure they get from doing it.
It's just us agreeing with The Punisher giving these people a taste of their own medicine, even though it can be in some pretty disturbing ways as well. Sometimes it takes a monster to get rid of a monster and The Punisher is the innocent people's monster.