If the Confederate flag is always racist no matter what, why didn't anyone view the Duke Boys as being Klan members when they flew it over their car?

Quite simple. Because of the people who owned the networks and held the balance of power. In a time when you could still lynch someone and get away with it you were not going to see much in the way of alternative viewpoints.

And I am confused why you think a fictional TV show somehow changes objective reality and historical facts.