back when i was road running alot (70+ mpw), i made sure to get at least 1 barefoot run in per week- usually a minimum of 5 miles. the trick is to find a good, dedicated spot to do so. around here at least, that means golf courses (who don't tend to be too friendly to the idea) or, luckily for me UT has an intramural field nearby that i could do 1 mile laps on. nicely manicured, mostly free of twigs and the other potential hazards.
think about it like this: while the human anatomy, in an evolutionary sense, isn't quite "there yet" in bipedal terms, we are fairly well developed, naturally, for this activity. while shoe technology has certainly come a long way, it still does one basic thing- it creates an artificial (non-natural) condition for your body. basically, it weakens a bunch of stuff in your feet and legs (like your achilles, for instance) by trying to protect your feet from impact. so for the sake of comfort (and, for a large number of people with inherent physical "problems", actual physiological benefit), running shoes end up causing atrophy in myriad muscles, tendons, ligaments, and the like. running barefoot, at least part of the time, helps grease all those little gears that otherwise get neglected.
that said, you have another option that's probably just as good- become a trail runner, if you have a trail handy. for the last 4-5 years i probably do 90% of my running on trails- the same rocky singletrack i ride as often as i can. it's slower, it hurts more at first (because it actively induces all those formerly passive muscle and ct groups), but once you get the groove- for me at least- it's infinitely more enjoyable than running loops around the city streets all the time.