I think most people understand this. In an alternative universe, where the Confederacy won, the confederates are the patriots.
But we don't live in that alternate universe, do we? We live in the USA: the country that declared independence in 1776, not 1860.
I'm not suggesting that confederate soldiers should be vilified. I realize that most had little choice in the matter. And I don't think regular German soldiers who fought against us in WW2 should be vilified. But, I think it would be wrong for the federal government to build monuments to honor them.
This not a place for moral relativism. The Confederacy was a morally-flawed slave empire. They fought a war to preserve their slave empire, and lost. We don't need to honor them.