The confederate flag is the flag of a rebel nation that went to war on America. Now does this mean we should just ignore it? Absolutely not, it's a vital piece of American history. It, however, should not be flown on any federal buildings. And Rober E. Lee was not actually a HUGE fan of the confederacy, he was a fan of his state. He actually believe that the confederacy should so whatever it can to remain in the union. He logic behind it was that breaking apart from the Union would be a direct slap/insult to the forefathers who created the constitution. Just a little interesting tidbit for ya.
Anyhow, just to sum up. The confederate flag is the flag of a rebel nation. Not to be outlawed, but not to be flown on federal buildings. The Civil War was not directly about slavery. Lincoln freed the slaves to break the Souths economy, which heavily relied on slavery.