They are in the civilized world, where everybody wears shoes with fat heels, and eats garbage. Take a look at places where people have to walk barefoot and you'll see a huge difference.
More relevant links: http://mtkfitness.typepad.com/mtk-fitness/2009/07/more-antis... http://www.dailymail.co.uk/home/moslive/article-1170253/The-...
As my medical history professor put it: "Have you ever noticed how in [American civil war] pictures, Confederate soldiers looked smaller than the Northern soldiers, like some of them were still kids? A lot of them had their growth stunted because of hookworm, due to walking barefoot." This was a major public health issue in the Southern US in the 30s. It still is in much of the world. Suggesting people run barefoot is pretty irresponsible, and shows how many things they take for granted - like people crusading against vaccination .
Also, a lot of peasants centuries ago ate poorly, too. Want an example? Read about pellegra in Italy, beri-beri, or how much alcohol was commonly consumed in colonial America on a daily basis. As counter-intuitive as it must sound, many peasants were poor, and weren't always able to eat well.
Humans moving to Northern climes traded the hazards of living in clothing for the hazard of living with endemic diseases (which both clothing and a colder climate warded off).
But I'd personally like to avoid both kinds of problems if I could...
Also, Pallegra wasn't a disease of the traditional peasant diet but was a result of the introduction of corn into the diet, a feature of development. (http://en.wikipedia.org/wiki/Pellagra#History)
Better example: When health-food advocates talk about how whole grain bread is more nutritious than bread made with just white flour* , they sometimes note that people favored white flour because of some elaborate cultural subtext about whiteness and purity. That's BS - it's because without refrigeration, the oils in the bran go rancid . Readily available whole grain bread is actually a modern luxury, thanks to transportation infrastructure and pervasive refrigeration. White flour has a much longer shelf life, so it was common historically - it's not junk people started getting fed recently due to some evil processed food conspiracy.
* Spoiler alert - it is, and it often tastes better.
(1) According to Wikipedia, "the usual method of infection is ... walking barefoot through areas contaminated with fecal matter". How often do you see fecal matter lying around in the areas you walk in? When I suggested comparing the "civilized world" with "places where people have to walk barefoot", I didn't mean that you look at /all/ aspects of those places. You can have your cake and eat it too - in the "civilized world" you can walk barefoot without having to worry about hookworm as much as you would in the developing world.
(2) If hookworm is still an issue, feel free to go with a middle-ground option like wearing Vibram Five Fingers. They're almost as good as barefoot while still protecting you from hookworm et al.
Have you ever been to San Francisco?
How about any city with any stray animals whatsoever? Have you never accidentally stepped in dog crap in a park? Fecal matter doesn't have to be human in origin to spread disease.
The fact that this story keeps getting reintroduced and the Vibram Five Fingers are always mentioned makes me suspect it's a marketing ploy, much like "the suit is back" / The Men's Warehouse in PG's "The Submarine" (http://paulgraham.com/submarine.html).