First of all, I agree with much of what you say here, Lasz2, regarding the issue of states rights and the confederates. I'd like to play devils advocate on one point. You mention that the acts of bravery of the soldiers "far exceeds any racial overtones of the war". Can this same criteria be applied to the Nazis? German soldiers did many brave things. Look at folks like Otto Skorzeny, for instance. Crazy, yes. An SS bastard? You betcha. Coward? Hell no!
Do those actions mean make it so that a swastika should be flown with pride by those proud of the 'brave actions and accomplishments of a scrappy little country the size of Oregon that took on the rest of the world and almost won'?
If the answer is no, which it is to me, I think that it's not because of any inherent moral superiority of one group over another, but instead because not enough time has passed for the 'romantic notions' to fully take hold.
Ask a Yankee in 1900 about the CSA, he'd shake his head sadly and describe the treachery, horrific bloodshed, and attrocities of the war. Ask a Yankee today, and he'll describe the brave, honorable southerners who were misguided but just doing what they thought was right. 50 years from now, people will look back at the confederates with the same glowing admiration given to the 'noble savage', the way people think of native americans today.
50 years from now, I betcha we'll see swastikas in (flying?) car windows, not because there are a bunch of skinheads taking over, but because the 'romantic image' of the Nazis will be where the CSA is in our heads right now.