Running with supported shoes promotes a heel strike (not always, but usually) and without shoes promotes a mid- or forefoot landing pattern. Therefore, it’s not as simple as taking off your shoes and going out for a run. Making this transition is a lot more taxing on the muscles in your foot, ankle, calf, hamstrings. It isn’t bad, but it is different and we’ve become dependent on the support of the shoes and it takes time to adapt to moving with less under our feet. Try writing a letter with your non-dominant hand and you’ll get my point.
I’ve been thinking about giving this a try (ie. running barefoot or with those Vibram FiveFingers), but I understand it is very different than running with normal shoes. Maybe after I finish the half marathon in May I’ll take a few days off to recover and give running barefoot a go.
This is a good introduction with helpful tips.