Hmm...well lets see if I can throw my two-cents out into there.
The Legend of Zelda is arguably a European inspired mythology. Like so many other stories, it has a white, blong, clearly european "knight" who uses a mythical sword to banish evil. It's really just a matter of sticking to the stereotype of the common mythilogical hero more than anything. If this game was based on African culture, than I'm sure Link would have been black with tribal gear and a mythical spear (or something to that extent).
In these type of legends, there is usually an evil league of creatures. These are established clearly as monsters without culture, or possibly even thought. These usually take the form of dragons, bats, goblins, etc. You could say that Moblins represent the jewish culture, but more that likely they just represent the goblin arch-type with some features of Ganon thrown in. In the original game, Ganon represented a pig, and they were pigs...it's not too hard to find the accosiation.
It's clear that Gorons and Zoras may have other actual human races as a sort of influence. The Zora's in MM have a jamaican look to them (the band ones) and the gorons have a tribe which is not unlike other cultures (aboriginal, african). These aren't shown in a racist light, because they are shown as strong people.
The Gerudo are clearly a lot like the islamic people. Not really in how they act, just their style. They act more like an amazonian culture. It makes sense too, the Hylians (Europeans) live in the green plains and the Gerudo (Islamics) live in the desert. They aren't shown necessarily as bad. Even later in OOT for instance, they take the side of Link and refuse to stand with Ganondorf.
But in the end, Nintendo really has made their own cultures without much resemblance of real life. It's a traditional medieval fantasy with other elements thrown in over the years to make more kinds of people in the game.
