Actually, the battle flag of the Army of Northern Virginia was square. While the modern Confederate flag was based on the battle flag, it isn’t the same thing. The modern flag came about many years after the war as a nostalgic emblem. If you see pictures of Confederate veterans, they all wear a uniform and the “Confederate flag” may be featured in the photo. But the Confederate uniform is also a post war invention. The Confederate units had different uniforms and sometimes no uniforms at all.
For more than a century the “Confederate flag” has been considered an emblem of the South. People who flew it may or may not have been racists but they didn’t consider it a symbol of racism. Civil rights activists may have equated the flag with the South’s resistance to civil rights, but a lot of hostility to the flag comes from people who simply hate the South. The recent hatred of the South is odd since so much of this poisonous bile comes from people whose ancestors arrived in the US after the civil war was over. And most of the ardorous haters are too young to recall the civil rights movement.
Yet they work themselves into a frenzy against people who had nothing to do with the Civil War or the Jim Crow era, and revile people who are long dead. Apparently the history of the Balkans teaches them nothing.