Third, while I agree with the majority on racism, the confederate flag has no special meaning other than those who cherish or distort its past
Whatever it's origins, this flag has been adopted by many racist organizations and people, and so has come to symbolize racial intolerance and hate and is offensive to a great many people. While some may chose to use it and they may have that right, there is no reason for any government to use it in any way.
It's just a shame that it took a horrific act to accomplish this.
If it's doing no harm, then it's doing no harm.
But it is doing harm. Imagine a person of color visiting a government building and seeing a symbol of the people who wish to oppress them. Why would that be OK for anyone? The swastika was adopted by the Natzis, so should we be OK with it being used today, just because it originally had a more benign use? Imagine a Jewish person seeing a swastika adorning a government building and tell me that would cause no harm.