There was no CSA flag flown at the state capital in SC until the civil rights act was passed in the 1960's. Then the segregationist leadership of that state, and others, responded by claiming that they could defy the federal government (just like they had 100 years earlier). And as part of this state's speech SC chose to begin to fly the stars and bars over their statehouse. It was a clear response to laws enacted to help black Americans achieve equality. That is not an accident of history. It is a clear message to black Americans. The CSA flag is no more a symbol that is legitimately used to honor the South's history of starting the most brutal war fought by the USA than flying the flag of Nazi Germany can be said to honor the German's who died for their country and fought out of German patriotism, perhaps not fully aware of the policies of their leadership.
The Nazi flag is of course still revered by some and its meaning is not German pride. The CSA flag is still revered by some, and its meaning is not Southern pride. It is not surprising that Mr. Roof on his personal website has photos of himself proudly holding the CSA flag while also burning and spitting on the American flag. You fly the CSA flag, you are speaking very clearly. You wish the CSA had won that war and that the darkies were still on the plantation.