The Confederate flag definitely should not fly over government buildings (federal, state, or local) because it is a symbol of treason. The only public/state owned spaces we should find this flag are museums, Confederate Memorials, and other historic sites. Even though I'm offended when I see it, what businesses and private citizens choose to do is their prerogative. It let's me know where they stand. I have a right to choose whether or not to patronize those businesses or associate with those individuals who fly this flag.
Personally I think those who choose to fly the Confederate flag are selfish, insensitive, and lack regard for the suffering and pain of others. I'd never display a Swastika (sacred symbol in Hinduism, Buddhism, Jainism, and Odinism which means good fortune). Why? Because I'm a Believer and I empathize with Jews. The meaning of the Swastika was marred by Hitler. A symbol of good luck became a symbol of evil.
Regardless of what the Confederate flag means or meant to some it was used as a calling card at burnings and lynching. It was used as a calling card of those who terrorized my ancestors. Your precious symbol of "southern pride" was marred by bloody, murderous, hateful, evil human beings who quartered people (took a living man/ woman, tied each limb to a horse and sent the horses in four directions), raped women and children, castrated men, desecrated dead bodies of those they murdered, etc. They left this flag to take ownership of their actions. Just as most terrorists leave their paraphernalia and symbols today. I get sick to my stomach thinking about this- not because I'm black but because I'm a Believer and lover of humanity.
And finally, removing the flag doesn't change hearts and minds. Those who love this flag so much even after it was marred and became a symbol of evil and who claim to be Christian should sincerely pray a simple prayer- "Search me, O God, and know my heart; Try me and know my thoughts. See if there is any pride, hatred, and bigotry in me, and lead me in the way everlasting that I may seek justice, love mercy and walk humbly with you God and all my sisters and brothers in Christ regardless of their race, ethnicity or national origin. In Jesus ' name. Amen." Shalom.