This is, in my book, real innovation.
"Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title."
If you were thinking of something else, I kindly ask you to make a point, instead of asking me to prove a negative.
I am not sure if f.lux is entirely non-obvious...
could we expect no more non-obvious apps like f.lux get made if the state doesn't guarantee decades-long monopoly?
There are themes for text editors which have both a day and night version (and some users will without a doubt have setup cron to switch automatically).
There are also blue-blocking filters recommended to wear at night for improving your sleep rhythm.
Of course none of this means that the f.lux author can’t obtain a patent on something related to his software. The question is if it will hold up if later disputed.