This particular car was an original car from the TV show and was previously owned by John Schneider, who played Bo Duke on the show. Bubba paid $110,000 for it at auction and it was in mint condition when he bought it. He also had it autographed by Schneider. The fact that it was one of the actual TV star's person car and was used on the TV show gives it increased collector value and provenance due to the documented history. And people do occasionally drive collector's items, because they are cars. They are meant to be driven. The worst thing on a car is to sit and never be driven.
The flag is most likely an automotive wrap grade vinyl application. Yes, it can be easily removed, replaced, etc. so no permanent disfigurement impacting relative value.
The issue is he bought the car because of what it is, what it was on the show, and his affinity for it and how he feels compelled to change that. Well, that's his car and he is free to do with it what he wants but it's no longer what it was on the show. Is he going to change the name of the car too? I mean, to have "General Lee" on the top is also offensive to some. Even if you change the flag and the name everyone still knows what it was. So why not change the numbers on the side and paint the car black? But everyone associates 69 Dodge Chargers with The General Lee, so perhaps he should turn it into a pickup truck.
If to a southern person the flag means "I'm from the south, we say yall and ma'am, drink sweet tea, and speak with a slow draw." Who is to say that someone else's assigned meaning is more important than the other person's? Inanimate objects aren't the cause of the real problems, and assigning various meanings to them or yanking them out of existence won't solve the real problems. Why people chose to put so much blame on an inanimate object rather than the crazed individual that committed the crime is beyond me.