I was okay with the government flying it in SC, because 1) it was the battle flag, for soldiers, not the political flag of the Confederate States of America and 2) it was flying at the memorial for South Carolinian soldiers who died in the Civil War. It's a sign of respect for the men who died fighting for their home and neighbors. Most of them were poor people who didn't own slaves themselves, and were, like every other damn soldier ever, fighting a rich man's war for the rich man's interests, but died believing he was fighting for home and honor. I don't believe they should be dishonored.
I can understand, though, Wal-Mart and pals not wanting to sell flags. That's fine. They can sell or not sell whatever they want (within the law). But Apple is just fucking stupid, pulling it from video games set in the Civil War. Might as well replace the soldiers' guns with walkie-talkies, too.