What are the disadvantages, apart from "massive callouses"?I can't edit my comment anymore, but my dad loves to run barefoot. I mentioned callouses as an excuse to link to a blog post where he shows off his Fred Flintstone feet.
As to the disadvantages... what if you're fighting Hans Gruber and he shoots a bunch of glass windows?
I think being barefoot all the time is very different from just running barefoot. A barefoot life is rather unsanitary and unsafe (there are lots of dirty pointy things on the ground). Shoes offer protection from cold, heat, physical trauma, sunburn, moisture, and social embarrassment. They also provide better traction on many surfaces.
I'm too lazy to go searching for sources that justify my claim, but you don't have to look far to find some weaker evidence. Look at people who have the muscular strength but not the structural support necessary to walk: they use braces to help restrict motion or devices to reduce weight on their joints (walkers, crutches). Look at anatomy: ligaments don't thicken along with one's waistline. Even if they did, they wouldn't keep up with the square-cube law.
I guess a more concrete example would be this: If you had to wear a weighted vest while running, would you rather be barefoot or wearing supportive shoes? If the vest is heavy enough, your calves won't support you and you'll be forced to heel-strike. At that point, a supportive and cushioning shoe would be less stressful than barefoot running. That's basically what people with weak calves or large guts experience. And most people in that situation aren't going to train enough to get to the point where barefoot running is better for them.