One could argue that the US flag represents the genocide and subjugation of the native American populations.
I play Panzer Corps on my iPad. As a WWII game, not surprisingly, there are plenty of Nazi flags in it. And there are certainly WWII apps with Imperial Japanese flags.
I'm pretty sure I could find an app with a Belgian flag, which represents a history of cruelty the worst American slave owner could never dream of.
I played an app called Roads of Rome yesterday. Didn't really care for it, but I don't think anyone would defend the Roman empire as a model of enlightened equality.
The point is that the Confederate flag is history. We could argue about whether it belongs flying over state capitals but to remove it from a historical wargame is lunacy. You want to pull an app from the store that is some sick exploitative game where you get to whip slaves or something, fine...but saying "whoa, a Gettysburg simulation is WRONG!" is just nuts.
For pity's sake, how many fantasy games celebrate racism - all that "orcs vs. elves" crap is racism, no? OMG.
Separately, people have seized on the Confederate flag as an evil and that's absurd. Yes, slavery was bad. But that was 150 years ago and in the interim, the Confederate flag has become a popular symbol of the South. Not everyone who has a pair of stars-and-bars underwear or plays with a General Lee car is a racist.
Of course, the real problem is not the flag but rather reconstruction. Why did we ever let the conquered peoples of the Southern states back into the Union? Why aren't Alabamans and Georgians paying me special taxes and doing my yardwork? Americans don't understand how wars work.