Over at the AV Club (where he's breaking down the season, episode by episode), Vince Gilligan said that the writers haven't developed anything more about Gus' background than what's been established on-screen. He speculates that it must have something to do with the Pinochet government, but unless a reason comes up to elaborate upon that on screen, he's comfortable leaving it a little mysterious.
Not gonna link them? It's an awesome set of interviews.

Part One
Part Two
Part Three
Part Four