Born to Run by Christopher McDougall is a very interesting read on the running potential found within the human species. He also talks heavily on the concept of barefoot running and how modern athletic shoes with heavy arch support and cushioning may actually contribute to the very injuries that they are intended to protect from.
My take on it is that the human foot is designed to run safely barefoot, with the caveat that the world we live in is often completely paved over which is an unforgiving surface on which to run. So yes, we are meant to run barefoot, but on grass, dirt, sand, and sometimes rock, but not strictly on pavement and nothing else. I think injuries can happen then, and my own experience seems to confirm it, for me at least. Run barefoot in the park, and sometimes on pavement. But not only on pavement.