I think I've mentioned it before, but here is my take on the confederate flag:
At some point, whether you want it to or not, certain symbols, words or actions take on a meaning of their own.
For example, prior to 1930s Germany, the Roman salute was just that, a military salute. We even used to use it here in the US when we said the pledge.
However, at some point, Hitler co-opted it into the Heil Hitler salute and we realized it now meant something different. No one tries to salute the flag like that anymore.
The confederate flag is the same thing. At one point, to a lot of people, it meant simply being "a rebel" or "southern heritage." And maybe it could still be.
However, watch the KKK or some other white supremicist group march or appear on TV and they have that flag. They have co-opted it to their own racist message. And its too hard to separate that.
So, even though there are a lot of people out there who honestly believe it means one-innoculous-thing, I think we need to realize that it now means another.