It doesn't matter how big or small the program is, appdata is not for executables, period!
If every developer used this logic "my app is so small, no reason ask user were to install it" the PC would turn into smart phone clone (although it seems windows is heading that way anyway)
How many Windows users out there that don't have admin privileges on their Windows PC? Perhaps by providing ability change installation directory it would allow install by non-admin and receive updates by non-admins. Or better yet - a portable version would kill 3 birds with one stone...
Regarding updates, there are two different approaches in software updates:
update notification with provided ability to install
forced update
A good software would use #1 and allow user choice if they want update or not (and perhaps even allow them chose if app should remember their choice in next update). Many users don't like fresh updates, because often it bring more problems and they want to see other users responses first.
f.lux unfortunately chosen #2, doing it without user's consent, opening a door for installing whatever it wants without user's knowledge, sorry, but that's exactly how backdoor trojans work...
"You simply cannot convince millions of people to update by hand, it doesn't work." that's precisely why #2 approach is bad, because a lot of people disable auto updates that happen without their knowledge and now have to update it manually.
[EDIT]
And f.lux team being an asshole, by giving negative reputation to posts they don't like, while we, mortals, can only give positive reputation...