That pic in the show notes isn't the Confederate flag. It's the the Army of Northern Virginia's battle flag. It was never flown over state capitals during the Confederacy.
It only became the symbol of the Confederacy, and the South in general in the 20th century. In the late 1950's, it was added to the state flag in Georgia as a protest against racial integration of schools.
The battle flag continues to be flown supposedly as a symbol of ancestry and heritage, but that wasn't its original purpose. The flag that many southerners feel pride for was actually rejected as the symbol of the Confederacy in the 1800's.
https://en.wikipedia.org/wiki/Flags_...tes_of_America