Rehashing the Confederate flag
To be picky about it, what is usually referred to as "the Confederate battle flag," isn't. The actual Confederate flag was square, not rectangular. Historically accurate flags, such as the one incorporated in the Mississippi flag shortly after the Civil War, recall the events of the Nineteenth Century, whether in pride or sorrow.
Later uses of the Stars and Bars from the 1950s and 1960s must be understood in the context of that historical moment. When the segregationists of the South in the mid-Twentieth Century called forth their flag, it was in effect a new flag for a new moment in history, fraught with the issues of that day, principally resistance to federal power mandating the end of segregation and Jim Crow and all the rest of it.
The two moments are connected, yes, but not by a straight line. Thus, I have no problem with States displaying the actual Confederate battle flag (the square one) at memorials and battlefields. The issues of that day are over and settled, and we should let the dead rest in peace. States displaying the modern "Confederate flag" (the rectangular one), however, are recalling not the wrenching outcomes of 1865, but the more recent outcomes of c. 1965. We are still living with those. I do not think any government entity should fly that flag.
As for private display, well, private citizens can do pretty much what they want. As the Supreme Court has repeatedly ruled, private citizens can even make the US flag into clothing, decoration, or toilet paper. That may offend others, but it's a private offense, not a governmental one. So, in popular culture today, the Stars and Bars (1860s version or 1960s version) pretty much stands for a kind of in-your-face cussedness, and as such should not be automatically understood as a racist sentiment. At the same time, the "outlaw" types who favor its display would be wise (and courteous) not to wave it in the faces of those for whom it will not be so understood. And they generally don't, I think.