The Confederate flag is literally a symbol of treason. Not only that, but the most treasonous act in the entire history of the United States.
Anyone who buys into the ‘States Rights’ explanation for the Secession either doesn’t understand what rights we’re talking about, or doesn’t care: the right to slavery. Elide motivations all you want, the southern states withdrew because with the entry of the western states to the union and the North blocking the expansion of slavery into the west, they felt their way of life and economic foundations being threatened. ‘States Rights’ is a euphemism for the right to slavery. If you disagree: off the top of your head list forme two other ‘states rights’ that motivated the secession.
Put the issue of motivation aside. What good came of the Confederacy? At the end of the day, their treasonous secession led directly to the death of hundreds of thousands, devastated the south, and increased the national debt from $60 million before the war to $2.7 billion afterwards! Why defend a symbol of such a wretched and shameful attempt to tear apart the United States? As you say, the only good I can think of coming from the Civil War is the Emancipation Proclamation. But somehow I doubt anyone’s flying the flag to represent that.
It goes without saying that individuals can do whatever they want on their own property— just as it goes without saying that I reserve the right to think you’re grossly insensitive at best and racist at worst and most likely—, but the Confederate flag should not be flown on government property.