In the Roanoke Times, Halford Ryan traces the history of the Stars and Bars. He concludes that its symbolism cannot be (you will pardon the expression) whitewashed:
But many recognize the flag’s disruptive symbolism for what it was then and for what it is now. They do not honor the flag now nor respect what it stood for then.
The Confederate flag in 1861-65 symbolized exactly what it signifies in 2014: rebellion over slavery against the United States of America.
Follow the link to see how he reached this conclusion.