Complex to a point. I don't think even the most rabid Greenpeace zealot would argue that Hitler's animal cruelty laws justified the rest of his actions. The Confederates had some noble ideals, even some noble actions, but they were implemented in one of the cruelest and most backward systems in American history. They're a prime example of the incumbent refusing to adapt to a changing world, hanging on tooth and nail until modern ways drag him down. With the advent of industrialization slavery was a doomed economic model, it was only a matter of time until it failed. But of course we had to fight the most costly war in American history to convince the Confederates of that.
And the problem is that things and people are not all good or all bad. When someone like Hitler comes along, they are easy to cast aside because the bad they do is so large that any good would not be worth it. It gets harder with someone like Lincoln, because he is far closer to the middle of good and bad.
The south was abused with other laws and taxes. They were upset by those, but seemed to be willing to deal with them. The threat of slavery was the final 1 ton straw.
The war was mainly about slavery, but it not not only about slavery. Resentment of the north and its policies was a very real thing. While 1% of Southerners owned slaves, it was a fact that most people saw blacks as being below whites. It was likely necessary to have that view, because if you saw the lives blacks lived under slavery, and you thought blacks were equal, you would be horrified. So while only a few owned slaves, everyone in the south benefited and racism was necessary to get over slavery.
The point is, the flag is not only about racism, but it was such a big part, that it would be stupid to over look it. The Nazi flag was not only a symbol of anti semitism. The Nazi movement was in large part due to the economy post WWI, but the anti semitism was obviously part of the beliefs. People will want to focus on the good, and ignore the horrible bad. Some will cherry pick the good to hide their racism, and some will believe racism has nothing to do with the flag.
This is why the government should get out of speech and only allow people to express themselves.