By now nearly every American understands that it is way past time to take down the Confederate battle flag, whose appearance outside of museums should have ended when Lee’s Army of Northern Virginia surrendered April 10, 1865. Confederates lowered the flag then, and their spiritual descendants should accept that.
That was the battle flag of the Army of Northern Virginia, not the flag of the Confederacy. It was designed to look sufficiently different from the American flag for Confederate generals to tell which units were friends or foes in the smoke of battle, after confusion in earlier fights.
I imagine that some advocates of the Confederate flag were startled and confused when they saw that website photo of Dylann Root waving the Confederate flag while burning the United States flag. A lot of people in the South revere the national flag, and drive trucks with bumper stickers threatening flag-burners. Let us hope that the photo of Root with those two flags damped some enthusiasm for the Confederate flag.
Confederate-flag advocates who believe in flying the flags of previous governments, legitimate or not, might try suggesting this flag, which was the first flag of the Confederacy.
But modern day Confederates might not be happy if other states and cities flew the flags of other governments that had once controlled the area. Imagine their response to seeing the Mexican flag, which could be flying in Texas, California, Arizona, and New Mexico. And they might not be happy with other historic flags representing countries that once controlled portions of the United States.