The Temptation of Adam

I have always been a little confused by what the War on Terror actually was/ is. Perhaps I do not understand terrorism, but I believe an oversimplified definition would be, violence used for political purposes. It seems like Bush really felt like he was waging a just war: "But he didn't do it [conclude the war was just] by combing through texts or presiding over a disputation. He decided that Saddam was evil, and everything flowed from that." He made his decision and then backed it up, which seems like backward reasoning. How is this different than what "terrorists" do? They say we are evil, we say they are evil. And both use violence to hurt the other one. So I'm being vulnerable here and saying, I don't understand how the 9/11 attacks were evil but the War on Terror was just, other than the later being retaliation.