Law of Conservation of Detail.
We only see the homes on Skyloft of important characters (for the sidequests and whatnot). Programming and just not-thinking-about-it means we don't get to see the homes of more random people, such as the knights...
... or the parents of most of the kids at the Academy...
We see Pipit's mom and we know Zelda lives at the Academy with her father there, but the rest... who knows? I have a little pet idea that Link might not be an orphan in this game - maybe he has folks, but they just live on an island somewhere and send him to boarding school.
When you think about it, there has to be more islands, even big ones, somewhere in the great blue sky besides Skyloft that you just can't get to because how do they grow food? People must live on more than just pumpkins! If the trees of Skyloft were the only source of wood they've got, they wouldn't be able to have shields, shelving, building materials...
Urk, thinking too hard without essentially "fan-fictionizing" it all will make your brain hurt.