In the above image, the Tower Hangar desktop, we can see the New Monarchy symbol on the large red banners. In [url=http://i.imgur.com/nrxV7T6.jpg?1]this image[/url], we can see what looks like a variant of the Dead Orbit symbol emblazoned on another banner. Both these images feature humans, so these faction symbols probably don't represent hostile races. Perhaps they represent the Guardian's version of [url=http://en.wikipedia.org/wiki/Chivalric_order] chivalric orders?[/url] It would fit with the fantasy/medieval themes of Destiny, and the idea of the Guardians being knights.
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to be honest, I always thought of the human guardians being against everyone else (cabal, vex, fallen). so what confuses me is why the factions would fight each other. i think it would be cool if there were factions, and that was incorporated into the multiplayer pvp aspect of the game, but not the main regular co-op play.