The rebel flag may well have some powerful meaning to 'rednecks' in 'the south' and will no doubt be read that way by kneejerkers but I feel that its use was in an ironic context on the show and that will certainly be the context within the new film.
I hate ALL kinds of revisionism and that includes censorship of the 'blackface' gags in Tom & Jerry cartoons through to Holocaust denial and on to Greedo shooting first.
[Rafiki hits Simba on the head with his stick]
Simba : Oww. Jeez... What was that for?
Rafiki : It doesn't matter, it's in the past.
Simba : Yeah, but it still hurts.
Rafiki : Oh yes, the past can hurt. But the way I see it, you can either run from it, or learn from it.
[swings his stick at Simba again who ducks out of the way]
Rafiki : Ha. You See?
But you can't CHANGE the past, so don't try.