Like other large retailers, including Amazon and Walmart, Apple is removing content containing depictions of the Confederate Flag, specifically apps and games in the App Store. According to Touch Arcade:

The reasoning Apple is sending developers is "...because it includes images of the confederate flag used in offensive and mean-spirited ways." We just spoke with Andrew from HexWar Games, who have released many historical strategy games. He insists, "We're in no way sympathetic to the use of the flag in an offensive way, we used it purely because historically that was the flag that was used at the time."

Touch Arcade also received a statement from Maxim Zasov of Game Labs, the developers of Ultimate General: Gettysburg, stating they accept Apple's decision to take down the game and that they recongize that the Confederate Flag issue is currently "a sensitive issue for the American Nation."

Apple's CEO, Tim Cook, spoke about the issue, broadly, on Twitter:

Like with any major policy shift with a retailer the size of Apple, there will likely be turbulence for the first few days. We might see some apps removed that shouldn't be, and some apps not removed that should be. Edge cases will be argued and opinions will vary. Hopefully most of that will be settled quickly.

Update: According to TechCrunch, Apple says it is working with some developers to have their games restored to the App Store. It's unclear if that means they will require changes first, or if some games with historical or educational value were mistakenly removed. In any case, the company seems to be mainly concerned with apps that cause offense:

Apple's intention is not to lose games from the App Store, but rather remove those titles that could offend. That means there will be some apps that are not likely to be reinstated, such as the banned Confederate flag wallpaper app, for example.