The thing is (for starters) those states seceded from the union because they wanted to maintain slavery. The claim is made that they were exercising their prerogative as states free of federal powers (or that federal powers were exercising undue prerogatives), but the contention between the conflicting prerogatives was slavery. A fairly solid argument can be made that slavery was unconstitutional, but an impenetrable argument can be made for the wholesale violation of individual rights that slavery represents (and the protection of individual rights is the purpose of the Constitution in the first place). The southern states had no right to maintain the institution, period. When I see the Confederate flag, that is the 'heritage' I see being represented. I don't understand what else it could represent. That they were fighting for their 'way of life' doesn't hold water. The only aspect of their way of life being threatened was the ownership of slaves.
So that was the stand they took, the flag they raised was an enemy flag, and the enemy lost the war. It's incomprehensible to me that it would ever be permitted to fly over an American governmental facility after 1865. I realize they are state facilities, but they are states within a union. But, like I said, that's just me. Clearly, the federal government has no intentions of forcing their hand. In the final analysis, they shouldn't have to. Honor should be enough for them to see the error their forebears made and take it down. Nikki Haley did the right thing, and she did it under appropriate circumstances. In light of the horror perpetrated by that racist scumbag in Charleston, choosing to strike the symbol (which is as much a racist symbol as it is a symbol of southern heritage) from state grounds sent the message that the flag did not represent the state of South Carolina.
Anyone who thinks they can decide for private individuals what the flag means and whether or not they can fly is an authoritarian pig, and they're brazenly tipping the hand of the entire politically correct zeitgeist. They are a demographic that could stand to learn from the historical example that was made of the Confederacy: your way of life does not give you the right to the lives of anyone besides yourself, and if you decide to initiate force to cross that line, you invite the equivalent retaliatory force down upon yourself.