I have two potential theories on this (well, I suppose more like speculation, but still) that relates to a previous mailbag question about why Link is wearing the green tunic in Skyloft when it's separated from Hyrule. I'll copy-paste it all here for you to browse and (likely) smash over the head. XD
"About the tunic (I know, there's tons of comments on this, but I haven't seen anybody say this yet):
Now, some of this is speculation, as it's impossible to perfectly piece together the timeline, but I think it's a fair guess nonetheless.
Now, starting with the Minish Cap. This is where we see, arguably, the earliest moments documented, for us, the players, of Hyrule. It shows the origin of Link's hat, a light force (likely before being known as the Triforce) and no sign of Ganondorf whatsoever. We are eventually introduced to the Wind Tribe, a group of people who once lived in Hyrule but moved from the Fortress of Winds to the cloudtops. These people are Hylian through and through, but the people of the Minish Caps' time have all but forgotten of their existence.
This, to me, sounds much like Skyloft. True, in the Minish Cap, this Wind Tribe still recalled their previous time in Hyrule, BUT, who's to say how much time has passed between Minish Cap and Skyward Sword?
I believe it possible that the Wind Tribe, after the events of the Minish Cap, grew to a much larger size in terms of population (or maybe the Minish Cap only gave us a small window into their new society). An entire continent in the sky could be necessary, and having been so disconnected from Hyrule, the new generations would grow up not knowing of the land below (informatio lost to time and all that), still retaining not only the abilities of the Wind Tribe, but the traditional ideas their directly-Hylian ancestors brought with them to the original Wind Tribes' home. After all, the Hylian hero has always been garbed in green, and if Hyrule had been around for ages even prior to the Minish Cap (as stated by the ghost of King Gustaf), who's to say there weren't heroes in green in ages past?
A quote from the beginning of Minish Cap:
"... when the world was on the verge of being swallowed by shadow... the tiny Picori appeared from the sky, bringing the hero of men a sword and a golden light *picture of a blonde male dressed in green, taking the sword with a Triforce piece hanging overhead*... With wisdom and courage, the hero drove out the darkness."
So, there you all go, that's my take on it: if the Wind Tribe kept /any/ customs of old Hyrule, it would likely be the hero garbed in green. Keep in mind, though, the "hero in green" idea seems to be destiny half of the time (I doubt Link in
ALttP was all "Imma be a hero, let's get me my green tunic out!", or the Link from Minish Cap thinking his green tunic meant anything aside from "I look like the smith I live with!"). It is entirely possible that this new Link simply wears green for the sake of wearing green. This theory, then, would still explain how he can be the hero, having been a descendant of the Hylians seen/heard of in the Minish Cap.
There is still room for another theory. If Skyloft has no previous relation to Hyrule, it could be that something terrible does happen there over the course of Skyward Sword, causing the destruction of the continent, leaving behind the City in the Sky we see in Twilight Princess. Over time, maybe, just maybe, after the events of the game (maybe during, but not likely), the Skyloftians begin to inhabit Hyrule due to the cleansing of the evil and the destruction of their previous home. Some may not want to leave their sacred floating island behind, however, attempting to adapt and rebuild their scattered buildings. It's possible the Skyloftians are the precursor to the Oocca; after the destruction of Skyloft, their bodies gradually evolved and adapted to the smaller humanoid birds we see in
TP (this would explain their out-of-place humanoid features while retaining their need to fly from place to place).
The Skyloftians now inhabiting Hyrule would have to start over, with new technology and new generations, but still retaining their Skyloftian knowledge somewhere. Over time, information is buried...
TP begins, and we see research being done on the Oocca, now seen as the "race closest to the gods, even closer than the Hylians". This line could refer to the fact that the Hylians, Oocca, and Skyloftians are one in the same, relating to "closeness to the gods" as a direct statement (Oocca and Skyloftians living in the sky, Hylians moving to the surface world below) as well as taking an evolutionary standpoint (Hylians being the secondary race spawned from Skyloftians, and Skyloftians/Oocca holding greater technology and adapting to remain, physically, higher than Hylians and closer to the gods). "
In other words (for those with no intention on reading all of that. =P), I believe it possible for the Skyloftians to be either the Oocca or the Wind Tribe. (Maybe both, if it's possible to combine all of that into one giant theory)