I'll weigh in a bit.
I am not African-American, and I'm not sure how many of you are, but all of us who are not probably shouldn't speak for them, and rather relay the message that multiple Black people have stated instead of opining.
However, I should say that it hurts me personally to see it flown because of the way I've seen Black friends of mine being treated by the White people that fly and wear this flag like it's a banner of pride. And growing up around both Black and White Southern kids and their families, I always knew that true Southern pride involves accepting people with love, good hearty soul food, twangs and "y'all"s, and the general acceptance that developed Southern people do not believe in racism or slavery or the Confederacy as being factors that define their character or stand as symbols for them.
The same cannot be said for people who enforce the twisted ideals of racism (which has manifested itself into a systemically disadvantageous way of life for people of color), who claim that we're equals but use the n-word as though it carries no implications or offense for the black folks that hear it. These are the people that fly the flag, usually. And these people scare me, their morals are the ones that some of our governmental systems have upheld with the guise of claiming "Southern pride", even though nothing of the sort is truly the case.
Historically, the flag has been used as a symbol for the Confederacy which fought for an economic system that stole native peoples from their lands, tortured and raped them, and used their hard work and backs as the foundation for this country. This includes much of the entertainment all of us enjoy both here and around the world. This flag has been used as a symbol by the KKK for hate crimes that directly targeted these humans, and many people like to conveniently forget that. This flag is an offense to see, and it has no place flying in front of governmental buildings.
When it comes to EPCOT, it's becoming generally accepted now that the flag and the history of slavery and subsequent hate-crimes should be showcased within a display, alongside words that respectfully describe the reasons why the economic model of slavery was adopted, as well as why the nation agreed after much strife that this was not an ethical model to support. It has a place alongside an apology, as does the showcasing of the erasure and forced assimilation of native peoples. But it should not be presented in the hall. As Friar stated, the experience is meant to showcase the good and the bad which I agree with, but to display such a tainted symbol alongside others is simply immoral.