I see this exact statement repeatedly and it concerns me. F.lux isn't designed to make things "easy on the eyes." If you're having that reaction, and you feel it as strongly as your post implies, it may indicate a different health problem.

You should consider getting glasses or altering your prescription. And if you're suffering eye fatigue it's probably not a great idea to be reading on a screen late at night regardless of the colors. Research "eye strain" for other suggestions that may help you.