It's a combination of pride, poor education and a hell of a persecution complex.

A lot of these people waving the rebel flag grew up in an environment where they were surrounded by like-minded people who encouraged them to take pride in their "Southern heritage" and brainwashed them with false stories about how the Confederacy was "innocent" and "unfairly persecuted."

On top of that, a lot of schools in the South tend to gloss over the issue of slavery in the Civil War, instead trying to claim that the war was fought primarily over states' rights (it wasn't).

In short, the people who were waving the rebel flag as they stormed the Capitol don't think they committed treason. They think they're the only "real" patriots. And that's the truly scary part.