It is worth the debate. It is historic after all. And I think they think it might encourage acts of racist violence, as part of the southern tradition. Whether it does or not, I don't know.
IMO its kind of the same as not using a swastika. Whatever people feel about it now, there is no arguing what it stood for. OTOH I don't think that ceasing to fly the Confederate flag will do anything to improve the US's problem with guns.
The Confederate States lost the War 250 years ago. The flag should not be flown on State buildings. It should have been discontinued years ago on official Government business.
If people want to fly it at their homes then that is fine, but it has been adapted by white supremacists rather like the extreme right in the UK have latched on to nazis iconography.
In fairness, England is still a country, albeit in a union. I may be wrong but I don't think the southern states ever was a single nation, it was independence for each state that they were fighting for.