You know things are bad when the pro-segregation rag National Review is locked in their own debate over whether the Confederate flag should or shouldn't come down in places like South Carolina. On the "get rid of it" side is Reihan Salam, who takes a look at the history of the symbol and notes that yes, its current popularity in the South had more to do with its rapid rise as the banner of the pro-Jim-Crow, George Wallace-era resistance to federal desegregation efforts than to the the Civil War itself.
[T]he use of Confederate symbols has gone through a number of different phases since the end of the Civil War, and the revival of these symbols that began in the late 1940s was about more than paying tribute to the Confederate war dead.
The column quotes the 2000 Georgia government report on the origins of its flag:
In 1948, the battle flag began to take on a different meaning when it appeared at the Dixiecrat convention in Birmingham as a symbol of southern protest and resistance to the federal government – displaying the flag then acquired a more political significance after this convention. Georgia of course, changed its flag in 1956, two years after Brown v. Board of Education was decided. In 1961, George Wallace, the governor of Alabama, raised the Confederate battle flag over the capitol dome in Montgomery to commemorate the hundredth anniversary of the Civil War. [...] Undoubtedly, too, it acquired a racist aspect from its use by the Ku Klux Klan, whose violent activities increased during this period.
So no, at the time the flag was adopted as a symbol of both the Klan and of general Southern "heritage." The heritage specifically being honored was the "heritage" of often-violent defiance against
Brown v. Board of Education and other federally backed civil rights victories. The battle that
particular flag was deployed to represent was the Southern battle against the Civil Rights Movement in the 1950s, not the battle of Bull Run.
Needless to say, this lonely appeal to plain history (and not distant history, but history that a nontrivial chunk of the modern conservative movement was alive for, and witnessed themselves) is no match for the resounding cries of nuh-uh, because shut up.
[M]uch of the reason the Confederate flag is so contentious is because objections to it are not raised in good faith. Many opponents of Confederate symbols demonstrate not to promote the reduction of racial tensions and the advancement of a shared good, but out of a desire to impose their own moral outlook on dissenters—because it suits their present-day interests.
Cite all the history you want, you won't convince the people whose own fathers and grandfathers first popularized the flying of the flag alongside the burning of the cross that it's about race. They're just pretty damn sure you're wrong and making stuff up, and that's all there is to it.