ok, lets do a little role-play, in order to explain my point.
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I am the leader of an evil team/group/faction/whatever. One of my underlings wins title that I covet. It is common knowledge that I made the evil group so I can win/keep the title. I kick underling from group & beat him up, because he has the title I covet.
5 years later, and now I have learned the errors of my previous evil ways, and have worked for the fans forgiveness (I became a good guy). My former underling, who never really did anything to become a good guy, is still evil. He, in an effort to win the title, threatens to bankrupt my families business, kicks my 62-year-old father-in-law in the head, kicks my brother-in-law in the head, and then assaults my wife; the only reason given was that he wanted to get "revenge" on me for kicking him out of the evil group I was in charge of 5 years before, that my in-laws/wife had NOTHING TO DO WITH. So now I go to defend my family from being further incapacitated, and seek revenge in their honor.
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Am I a bad guy for defending my family? THE ANSWER IS NO, and if you think otherwise, you are not using your brain. The role-play above is the EXACT SAME THING AS HHH/ORTON, just without saying who is who, in order to prevent bias against HHH. If you think Orton had a reason to assault the McMahons, you are gravely mistaken. Attempting to fire someone is not cause for assaulting their boss, otherwise we would have CEO's in the hospital every day, so Vince's assault is inexcusable. The kick to Shane's head was WELL after the match ended, so there is no excuse for kicking Shane. Stephanie is a woman, and as we all know, there is no excuse for assaulting a woman, even though she slapped him; last time I checked, slapping someone is not supposed to be as painful as a finishing move. So no excuse for Orton there.
Orton is the bad guy in this case, that doesn't mean he isn't talented, or he shouldn't have fans who appreciate his talent (I am one of them). However, his actions make him a bad guy, and because of that I would boo him if I was at a live event. Also, as modest-genius said, cheering him is the worst thing you can do for a bad guy. I also believe that Orton said the same thing in an article on ESPN.com, so you should boo him.