Because it makes for a boring story.
I personally think HFY is a misguided response to the tendency to cast humans as the "jack of all trades" species/race in most settings.
Because let's be fair now, humans aren't really portrayed as weak or helpless. Even if they're physically or technologically inferior to other species, because they're the protagonists they win anyways. Maybe through guile. Or moral superiority. There is always something that makes humans, in the end, better.
But clearly there is something out there that isn't quite sitting right with a lot of people. And while I don't like HFY, I think this feeling of discontent is very much real and justified.
Y'see the problem, as I mentioned before, is that people would like a clear identity. Not unlike nations or cultures today (note, for example, how offended we Canadians get when people say that we have no culture, that we're just "part of America").
So the thing is, when humans get portrayed either as the all-around guy (usually in fantasy) or inconsistently (usually in sci-fi), it often gets people the feeling of "what the fuck are we supposed to be." Humanity Fuck Yeah generally tries to say what we are. The problem is that all it does is replicate the initial conundrum. There are two kinds of HFY, I've found. There's the "humanity as a kind-hearted, brave, or otherwise touching species that inspires a certain sense of wonder or love in the aliens they meet" (such as that story with the little alien and the cigar) and there's the "humanity as the physically or technologically superior powerhouse" story.