The KKK was hiding behind the American flag in those instances. The American flag never stood for the KKK in the popular mind. You could never put out an American flag in hopes of attracting the KKK.
With the stars and bars the opposite is true today. There’s a conflation of its historical role where it was used in a specific place and time, one that no longer exists, and its use today as a rallying point for an underclass of disaffected losers who erroneously believe that they would be winners if only the slaves had not been freed and that there is some way to go back.