So... about that flag.

The Confederate flag waving on government property has been raising eyebrows for decades. The flag has flown atop or in front of the South Carolina statehouse in Columbia since 1961. So why the controversy now? It seems to be quite directly due to the racially motivated church shooting in Charleston, South Carolina. People seem to directly blame such violence on the historically explicitly racist symbols and names adorning the streets of the south. To me, that seems like a shift of blame that is as counterproductive as blaming the Columbine shootings on video games or rock 'n' roll.
The flag is not responsible for the Charleston church shooting. Rather, both are products of southern exclusiveness and isolation by ego centrism.

The days in which the flag was purely the banner for team slavery are long gone. It is now simply the flag for a certain subset of people living in the US. However, that doesn't erase its history.

Consider for a moment the swastika. It used to be a symbol of fortune, a token of good luck. I could wear a shirt with a big ol' swastika on it and use it to mean what it used to mean pre-Nazism. However, this is clearly not how people would read that shirt. Even though my intent would be nothing but good, people would still be hurt by the heavily negative emotions and actions associated with that symbol.
Reverse the chronology and the Confederate flag has the exact same problem. Most of those who wave the flag today don't do it to conjure up images of institutionalized racism, but rather images of neighborly barbecues and songs by the campfire. That isn't the case for those outside of that culture where most do perceive the flag as threatening due to its racist history.

So, the same way you might wave a swastika around in India and not in Germany, maybe flying the Confederate flag in the United Stated is not the best of ideas. But again, implying that the flag and symbols like it are the cause of the problem is taking the influence of the flag way too far and is ultimately detrimental to finding answers to situations like these.