I love my five fingers shoes and my minimalist (thin-soled) ones too. I hate thick soles and I walk a little funny, so being as close to barefoot as possible makes me happy. While I understand the argument that we evolved running on the Sahara (see Christopher McDougall, he's huge in the movement), it overlooks the obvious fact that we also made shoes for a dern reason. Ötzi the Iceman's footwear was so nice that folks are pretty sure that 5,000 years ago there were specialized cobblers.
For me, it boils down to the individual's biomechanics and preferences. I like to be barefoot -- my feet tend to sweat and get calluses all over them in shoes. Unfortunately society and my wife don't like barefoot people all that much, so I wear flip-flops or my five fingers. At work I have to wear a close-toe minimalist style shoe.
As far as running barefoot, that's an acquired skill in today's day and age for most of us First Worlders. I spent 5 years in the army, so I'm used to running (even though I'm soft and a bit of a fatty now, thanks to not having to do PT at 0630 every day anymore) -- but running in my five fingers was a big change for me. Muscles had been activated that hadn't really been used that much before. My calves in particular were very sore. It was a challenge to run differently (I've always been a sloppy runner -- poor form -- and I tear through running shoes).
But hey, as dorky as those toe-shoes are -- I like 'em! ...even if nobody else does