Which Confederate flag? There were numerous types. I will assume you mean the "Stars and Bars," or red background, blue "X" with white stars. It means to me what it really symbolizes - a battle flag of the Army of Northern Virginia representing the thirteen states of the Confederate States of America. That is what it meant then, and even as an artifact, that is what it should mean now.
I want everyone to take a look at the linked flag below. What do you feel when you view it? Does it represent racism and slavery? Oppression? Violence and war? No? Why not? If that is how you feel about the Stars and Bars, then that is how you should also feel about the Bonnie Blue Flag, as it was an exceedingly popular, unofficial flag of the Confederacy representing the Republic of West Florida. Fly it above the capital building in Tallahassee and no one, except maybe the very scholarly, would protest. Fly the Stars and Bars and you'd have Jesse Jackson, Al Sharpton, and probably the president himself condemning the act and wallowing in the publicity.
Something else this flag represents to me is the hundreds of thousands of Confederate soldiers and civilians that fought, suffered, and died during this Civil War, which was the bloodiest and most terrible conflict in our nation's history. I would expect these people to be memorialized, but not with the flag of their enemy.