I don't quite understand the comparison of the Confederacy to Nazi Germany either. I understand the need to try and make them seem as though they were identical, or at least similar, but I don't think they were either one.
They did lose the Civil War, however. And, it would help if people observe that they lost, and believe that "the good guys" won, and therefore not a lot of need to glorify the Confederacy, or what it stood for, fought to maintain, or has represented to most of society since then. If you're not convinced the United States "should have won the war", then it will continue to be an issue.
As far as 9/11 statues, there are never going to be statues of the terrorists (I hope not). But, maybe in 150 years, or so, the terrorists will be seen differently than they are now. I don't agree with the actions of terrorism. But, I certainly understand the motivation. Unintended consequences are not always pleasant. As long as they believe the USA (and the West, in general) is responsible for the chaos in their homeland, it will just continue.