Amy's parents were lost in the crack in time, just like everyone else in the Universe except the Doctor and his companions; her parents just disappeared a lot earlier (at least, along Amy's personal time line) than most of the others. After Big Bang II, all the people lost in those cracks were re-created, including Amy's parents. No good explanation has been given for this; but the Doctor has indicated that there's something extremely exceptional about Amy, which made it possible. The Doctor indicated that growing up next to a crack in time is at least part of what made Amy special, but I suspect there's a lot more to it.
I suspect that we'll find out some of the "lot more" during Series 6. It seems likely, though, that we won't find out everything until the character is about to leave the show. I'm in no hurry for that.