I can't believe I missed this. Christopher McDougall (author of Born to Run) has a good discussion on the barefoot running debate that is worth a read. Ultimately, I think it all comes down to a single quote:
But ultimately, the debate isn't about Bare Soles vs. Shoes. It's about learning to run gently. Master that, and you can wear — or not wear — anything you please.
— Christopher McDougall
This is essentially what I've been telling everyone who asks me why I run barefoot.