One way of looking at the barefoot thing is as a specific way of strengthening your feet. A mate of mine, who’s a triathlete, aims to to a couple of 20-30 minute sessions per week in FiveFingers on soft ground, but does the bulk of his miles in more conventional running shoes.
Personally I run in anything from very light trail shoes – Inov-8s etc – through to full-on cushioned shoes from Saucony. I kind of choose depending on how I feel, where I’m running and what I’m running on.
My personal take on it is that there’s a continuum from really cushioned road shoes at one end through to minimalist, barefoot things at the other and which works for you is down to personal preference, experience, how you’re built etc. No right or wrong answers, just what works for you.