Well, it could be for many different reasons. Perhaps the Goddess did a bit of a "Noah and the Arc" type deal. She took multiple species alongside the Hylians and brought them up to Skyloft so they could be saved. They may have been separated due to conflicts between certain groups. The Goddess may not have thought it entirely through and some of the less intelligent ones may have starved or even fallen off their floating island. It's possible that entire species died like this. This would leave many floating islands waiting to be explored by Link.
Or it used to be a single landmass. For whatever reason, bits and pieces of the land broke away but kept the floating properties and then formed a sea of floating islands. I think that it's very possible that this happened; Earth once had a single landmass as well. Of course, I have a concern towards that possibility. If they just broke off, then there will be minimal contents on the island, very much like on islands in the Great Sea.
I feel that the islands will be a good addition to the game overall, but I fear that some of our hours of exploring may just leave us with a single heart piece or rupee here and there.