This isn't a case where Apple did something incredibly arbitrary and capricious and then immediately ripped someone off (such as if they kicked all poker games out of the store and then included their own poker app). Apple enforced long standing app store rules.
F.lux legitimately deserved to get yelled at, they used private APIs and attempted to circumvent the app distribution system. Both were against the license agreements you have to agree to if you want to use Xcode.
Obviously you can argue about whether the rules should exist, etc. But there was no question that what they were doing would be 100% shot down.