Long time WDWMagic lurker who feels motivated to make his first post about this topic:
The issue at hand is the Confederate Battle Flag (i.e. Battle Flag of Northern Virginia) which is found in the canton of the flag in question (upper left hand corner). Unlike the "Stars and Bars", which was not removed from the hall of flags, it's legacy did not end at Appomattox Court House in 1865. Rather, the Confederate Battle Flag is alive and well today in multiple places in our country and abroad. It is used by many as a symbol of white supremacy and re-segregation. It has been for decades. It was even used a symbol of Governments in many Southern States to lash out against the Federal legislation brought about by the Civil Rights Movement (the very movement which is honored in AA's Golden Dream montage). While many have turned a blind eye to this fact, the recent church slayings abruptly and correctly placed this fact back into our national consciousness. It is a current, living symbol of a belief system that undermines the very liberties and freedoms our country is founded upon.
I also understand that to many, this flag represents only the history and heritage of southern pride, NOT white supremacy. However, until these people put the same amount of effort into identifying and stopping those who promote their flag's current symbolism of hatred and bigotry as they do in defending their right to fly it in their yards, on their cars, and at sporting events; I fully support any person, corporation, or government that chooses to remove it.
The current symbolism of that flag does not deserve to be legitimized by being given equal status among the others in the hall of flags. And unless Disney decides to allocate some money to the AA pavilion to provide guests a deeper social context of that flag, and the symbolism/actions it has promoted through reconstruction, Jim Crow, the Civil Rights Movement, and still promotes today, I am good with them taking it down.