They were rebels, and they are traitors to the United States. Nations normally don't honor traitors
Traitors like George Washington, Thomas Jefferson, Benjamin Franklin, et al?
If the South had won their independence, Robert E. Lee and Stonewall Jackson would be even bigger heroes.
Great Britain didn't honor those men after the revolution, considering them traitors to the crown and, from their point of view, rightly so. Likewise, had the south won their rebellion you might have honored Lee and Jackson but I doubt the North would have.
I think the fact that Lee and Jackson are still honored today in the North as well as the South speaks to how noble these men really were. If they had fought for white supremacy, these men would have been about as revered as Hitler and Himmler.
When it comes to the Civil War War for Southern Independence, much of that history has indeed been rewritten by the victors. However, it is comforting to see that though the South has been vilified over the past 140 years, the character and reputation of men like Lee and Jackson have been able to stand the test of time.
It is also interesting to see the comparison being made here between the CSA and Nazi Germany. To me, that simply means the Northern revisionists are running out of ammunition. They can't make their case logically or constitutionally so they have to resort to demonization. (Frankly, I can't believe WhiskeyPapa posted this article. I find it difficult to believe that even he subscribes to this point of view!)
Perhaps someone should introduce Asa Gordon (and WhiskeyPapa) to Maj. Willie Levi Casey Jr. of the U.S. Army.