When I was growing up, a friend of mine from the neighborhood once told me that he wasn't allowed to watch the show, "Hogan's Heroes" on TV. He said his father had been in a POW camp in Germany during WW2 and was deeply offended by that show, because it depicted the German Commandant and the guards as big-hearted fools, when they were anything but that. They were highly intelligent, well-educated, and they were ruthless. And there was nothing humorous about his time spent in the Gulag. He did not appreciate Hollywood making jokes about such a terrible reality. He felt it made light of it and thereby paved the way for things like that to happen, again, in the future.
There are some good reasons why people resent the confederate flag and what it stands for, even when it's just being used in a silly TV show, for entertainment. The Civil War was by far the bloodiest and most traumatic war in U.S. history. And it's not unreasonable that some people would find it highly offensive to misrepresent it, and make light of it, for fun, for entertainment, or for some silly redneck icon. As doing so does cause us to forget the horrible reality of that war, and of the lives wasted in slavery, and of brother fighting brother to the death in the name of economic exploitation.