Reconstruction was a period that was much hated by the majority of Southerners. It was Reconstruction that cemented the Southern States as the Democrats' "Solid South." For example, when the "Carpetbaggers" were removed from power in Texas in 1876, practically no Republicans were elected to statewide office for 100 YEARS! The "Solid South" enabled the elections of Presidents Wilson, Roosevelt, and Truman. Today, the "Yellow Dog" Democrats (whose name comes from the saying, "I'd sooner vote for a yellow dog than a Republican") have mostly passed from the scene, but there are enough left to effect a really close election in a few Southern states.
The current challenge for the Republican Party is to chip away at the current knee jerk Democrat voters, who must become convinced it is Republican policies that are the best for all Americans, regardless of race or color. I guess Ken Burns is afraid of just that.