To be fair, that's mostly 'cause "how are you" and its reply "fine, thanks" are emphatic. People generally don't mean "how are you" when they say it, they usually just say it as another way to greet someone.
So replying "fine, thanks" isn't really a lie as much as it is just replying to the greeting.
It's in the same vein as replying "good morning" to someone, even if you're not having a good morning.
Linguistics are fun.