As someone that has grown up in the south and is more than a few years old...no, that is not the case.
Cayenne... are you black? Because, to put it bluntly, horrible oppression is often a sweet deal for the oppressor. It's how it gets their willing participation in horrendous crimes, especially if it can outsource the direct application of violence to sadistic thugs and let Joe Average pretend he's not doing anything wrong, despite it being Joe who supplies the truly vital ingredient: legitimacy.
This uproar and associated meanings with the Rebel Battle Flag is a recent occurrence.
No, it's not. The flag has always stood for racism and slavery. The uproar is new, simply because the concept of civil rights for the blacks in America is.
I grew up with it and it was never that way....it was a backdrop for a Lynyrd Skynryd concert, or the top of the General Lee.
The Nazi flag was a backdrop to the Olympics, once. The people who watched them were unlikely to be any worse than the average person anywhere. They went home with golden memories of a wonderful day. But the culture that flag stood for was still monstrous.
Harmless symbols of southern pride.
And southern pride was about keeping oppression going even after military defeat. It's not harmless. It is, in fact, murderous.
The Allies forcefully de-nazified Germany after the war and forced the people to confront the truth. Unfortunately, the North couldn't force the South to repent, since it was just barely better itself. This terrorist attack is simply yet another surfacing of that lingering taint, a spring that keeps pushing poisoned water from endless aquifers, a weed that can keep growing back forever since the roots remain in the ground.
All this because one jackass that killed a bunch of innocent people had a picture of him holding a small version of it.
Southern culture contains structural violence embedded to it by its history. Everyone who takes it in - as everyone must, growing up - also takes in the poison. Some manage to avoid the worst of it and are relatively fine, while some turn into Ku Klux Klan fodder. And if a particular mind happens to be particularly vulnerable, either inherently or because of the specific conditions they're in, their own personal identity can take a backseat to one of the archetypes of their culture. In the US, especially in the south, one very prominent archetype is the racist lyncher who kills any blacks who get "uppity". That's the archetype the entire Confederacy was founded on. It's all there ever was to it.
Roof may be a "jackass", but he's also the embodiment of Confederacy as it truly was and is. Nations come and go, their spirits tend to live on, sometimes with their own name and sometimes as seemingly random aspects of culture. And the Confederacy's spirit is still alive and inspiring the only thing it ever stood for: tyrany.