Since it is relevant, and before the thread completely devolves, I will reprint here what I wrote on Facebook concerning this matter:
As to the actual question on hand, I really don't have a strong opinion, and even if I did, it would not matter, because it is a matter for private individuals, companies, and voters to decide.
What I am actually more disturbed by is the degree to which popular sentiment is able to overrule historical fact. I don't mean that in a partisan manner- it goes both ways.
For example, I have only read one quotation in which the flag in question is properly identified as the Battle Flag of the Confederacy (it was not the only one, by the way). People seem to forget that the flags of the Confederacy (there were three different ones) are different. The Battle Flag itself only became the primary symbol of the Confederacy after the War. On a side note, some accounts claim it features a Saint Andrews Cross instead of a Saint George's Cross because the designer did not want to alienate Southern Jews.
After reading up on the debate, I happened upon yet another flag dispute: the use of the Gadsden flag. Some apparently claim it is racist and is only a substitute for Confederate flags. They base this claim on two assumptions: 1. the Gadsden flag is inseparable from the Tea Party movement, and 2. the Tea Party movement is racist. The first one is patently false: the flag is as American as the American flag. It was invented by a South Carolinian during the American War for Independence, and many governmental and civilian organizations continue to use it. The second assumption is open to interpretation, but false in my opinion.
All of that said, remember this: the Confederate States of America was an enemy of the United States of America and the Confederates were rebels. The United States of America won that war and won with it the right to call the Confederates traitors. There have been many failed causes in history worth honoring, even mourning. There have been many more that we would rather distance ourselves from. America is (and hopeful will thus remain) a free country: it is your prerogative to choose for yourself whether or not YOU want to honor the Confederates as failed rebels or remember them as traitors.