The thing is that symbols change meaning. Many flags have been the symbol of terrible things today. Union Jack is still used today, even though it was the #1 symbol for so many atrocities.
Of course the confederate flag was originally the flag used in the war to keep slavery going. How many countries have fought wars on terrible grounds, using their current flags? All of them?
The way I see it, the whole basis of the US was founded on white men who owned slaves, a religion which advocates killing, and the genocide of native americans. The confederate flag isn't alone in this.
The current American flag was literally the flag used to eradicate native american people, that's the flag the soldiers fought under. But we understand historical context, and that it's not what it represents today. I think people should be able to do the same with the confederate flag.