When you have someone like Tim Cook say he thinks the flag is a symbol that feeds racism, it's going to be a tougher thing for Apple to ever bring those apps back. Really, It should be a tough thing for any retailer to bring them back.
I'm not going to speak for people who love the Confederate flag, but saying that you like the flag for the 10% that it represented is insane. You don't fly the Confederate flag because you believe in states rights. Just like you don't fly a Nazi flag because you believe in a strong Germany and you don't read Playboy for the articles. They're all piss-poor excuses for avoiding saying something you'd rather not admit.