What everyone seems to forget is that the Confederate battle flag IS an American flag. It's just as American as the yellow "Don't tread on me" flag, and it has a history behind it that won't go away just because some people's sensibilities are flustered.
Whenever someone says that they don't want the Confederate flag flying over American soil remind them that it was Americans that lived and died under that flag.
That's what happens when you have a civil war. You get people of the same nationality fighting against each other, often because some of them don't want to be part of the same country as the others. But civil wars are generally the bloodiest and bitterest of wars and people rightly want to make sure that they stay in the past.
In Russia today they fly the older Russian flag which was the national banner from the late 19th century to 1917. If more and more people start to fly the Soviet flag, it's a sign that their country is in real trouble and that people have forgotten history, even though strictly speaking the Soviet is a part of their history.
If you start seeing Mexican or La Raza or African nationalist or gay rainbow flags flying instead of United States flags in public places, it would be a real sign that our country is in danger of falling apart. People aren't wrong in seeing something disturbing in giant confederate flags flying in place of the US flag.
For much of the 20th century people didn't have much of a problem with the Confederate flag. It was presumed to be a symbol from the past that simply retained a regional nostalgic appeal. That was pretty atypical of how nations and governments work. French governments or mobs would have gotten nervous or violent at seeing too many royalist flags flying, and Latin American peoples or governments probably wouldn't have put up with many Spanish or United States flags over their soil, but few objected here because Confederate flags were assumed to be uncontroversial symbols from the past.
But those years in the early 20th century were days of Jim Crow. Over time the Confederate flag became a symbol of resistance to desegregation. So you can't just naively fly the flag now, like the Pine Tree flag or the Don't Tread On Me flag. There are questions that Confederate flags raise that those other banners don't. Flying it is very definitely making a statement, though people will disagree about what that statement is.
The fact that Americans fought, died, and killed, under that flag doesn't make it neutral or acceptable to everyone, since people understandably fear that what happened once might happen again. Nor is it a neutral symbol from history, since so many people disagree about just what history that flag represents.