Most of the people who use f.lux would not know whether they should have it start automatically when they turn their computer on. For users like you and me who don't want it to start automatically, yes, it's not convenient to do what it takes to make sure it doesn't start automatically but there is really only a handful of us in the crowd of f.lux users who don't want it to start automatically.
What's worse is, the average f.lux users wouldn't know how to get it to start automatically again due to forgetting where they found the setting. Every day on here would be a facepalm from the question being asked over and over and over, "How do I get it to start automatically again?" Or worse, "It doesn't start automatically and I don't know why" (because they are the ones who set it that way but they forgot that they did).
It's sort of the same design philosophy that Apple has. The less settings a user can change, the less likely they will create an overall experience that they hate and can't undo because they forgot how they created the overall experience they now hate.
I can tell you how to make f.lux stop starting automatically with Windows, but it requires you to delete something out of the Registry.
