Robert E Lee was the Supreme commanding General of the Confederacy, which seceeded from the United States out of fear that Lincoln and his new, progressive Republican party (times have obviously changed) would outlaw slavery.
The resulting Civil War was by far the deadliest conflict the US has ever been in in terms of US casualties. But the bonus is that since the war over slavery had started anyway, we went ahead and outlawed most slavery while we were at it.
Anyway, a lot of states, especially in the South kept discriminatory laws on the books following the war. As the Civil Rights movements of the 50s and 60s approached, a lot of Southern cities and states started building monuments and dedicating government buildings and parks to Confederate "heroes" and leaders.
They romanticized the Confederacy as a major part of Southern heritage (even though it lasted less than 5 years), and rewrote the history taught in schools to teach that the war wasn't about slavery, but about the federal government trampling on states rights.
And it worked. Millions of people are brainwashed into thinking that the rebel flag is a racist symbol, but a symbol of individualism and freedom. They tricked generations of Southerners into thinking they aren't racist.