no-one is seriously suggesting that anyone starts running without shoes – that's just silly (we live in a world full of dog poo, sharp rocks and broken glass).
but there is a lot to be said for running with a 'barefoot technique'
ie, not landing heel first. but instead landing on your forefoot.
this video shows it quite well
lots of people (i'm one of them) find that running with a heel strike causes a few problems. and so i have started running in very simple shoes which force me to run 'forefoot'. it is hard work on my calf muscles, but doesn't irritate my long-term foot injury.
the nike 'free' aren't really shoes for forefoot running; they've got loads of heel cushioning. what they do have is a very flexible sole.