People care when the confederate flag is flying over a state building because the state is representative of all the people, not merely a portion and a great many people regard that flag as a symbol of hatred and ignorance. Add to that the fact that almost all the southern states didn't start flying the confederate flag over their state houses until the mid-1960's during the fight over civil rights and it becomes clear that the claim that the flag was raised to honor southern heritage is a lie. It was raised to symbolize opposition the racial equality.
Also, it's not accurate to say that "southerners" want to fly the flag. Over one third of southerners are black people who feel nothing but contempt for it and a significant percentage of white southerners think it's time to put it away as well. A vocal minority want to fly it still.
If some bozo wants to fly the confederate flag on his private property or on his truck or whatever, then I agree that it's his business. Personally, I think it's an advertisement that he's just trash, but as long as he and his buddies don't show up at my house in the middle of the night, I couldn't care less.
That flag could have more than one meaning.