Although Apple are perfectly within their rights to do what they've done I hope they'd reach out to the f.lux authors and do something for them. It's not like they're destroying a business - f.lux being free - but it would reward the authors for proving the value of the improvement to the platform. You want to encourage developers like that. And it's not like Apple are short of cash.
Their web page still says "f.lux is patent pending."
Apple's "Night Shift" is great news for f.lux. If f.lux can get their patent then the billion dollar target is square in their sights.
I haven't seen anything on what exactly they are trying to patent to guess if Apple is infringing, but it does appear the f.lux business model is to get users hooked on white point shifting then profit from the patent.
The fact that f.lux is free does not mean it is not a business. Even though it is free they would be a multi million dollar business from my estimate. And Apple are indeed trampling on it by doing what they did. I'm not commenting on the morals of the whole situation, but it does seem necessary to clarify that it IS a business. Just because something is free doesn't mean you can't make money out of it in other ways.