Wow, by the logic in this article, I should have been dead (or at least infested with a healthy supply of intestinal worms) by the age of 5!
I HATE wearing shoes. When I'm at home, I don't. I muck stalls, muck out my chicken coop, run around in the woods with the dogs, garden, and do pretty much everything else outdoors totally barefoot. I even ride barefoot. Not dead yet!
When I was a kid, my friends and I had horse-poop fights. We would go out and grab dried up horse turds with our bare hands and throw them at each other. We're all still kicking.
I regularly take gross things out of my dogs' mouths and don't wash my hands. When I'm outside, working, Chief's favorite thing to do is to grab a horse turd and covertly hide it in the back of his mouth, sneak up to me, and then drop the slimy thing on me. I wipe it off, wipe my hands on my pants, and keep working- it would be dumb to walk inside, wash my hands, change clothes, and drink a gallon of bleach before going back out to dig in the dirt or shovel horse crap.
I feed my dog's raw meat and I wash my hands real quick after I handle it- and the only reason I'm vigilant about that is because half of it came from the store and I don't know where it's been. Meat that I raised butchered and cleaned myself? I'm much less worried about germs and bacteria, but still wash my hands because they're covered in meat juice.
I do taxidermy as a hobby, but only on things that I butchered for meat or died of natural causes. It's pretty common for me to be elbow-deep in gore at some point during the day. If I'm doing it outside, I generally just rinse off with a hose when I'm done, maybe wash my hands with soap when I get back inside.
My dogs lick my face, probably after they've licked each other's butts, and I don't die from it. People with pet rats commonly let their rats lick their tongues and clean their teeth (It's called rodentistry!) and so it's common for me to have a rat stick its head and possibly its entire torso in my mouth at some point during the day. Still alive!
When I was a little kid, I hung out with horses all day. Nothing I did was hygenic or safe. I had a habit of sitting UNDER my favorite horse, using him as shade, and reading a book while he grazed. He was careful not to step on me, but I got peed on once or twice. I didn't want my mom to know what I was doing so I would actually wait until it dried before going inside, and then I'd wash the clothes myself. So when I was about six, there was a good chance that I was spending half of my day covered in horse pee, riding some random horse bareback with just a fist full of mane to hang onto, (and guess what, no safety gear!!) resulting in me falling off ALOT. Then after I got tired of falling off I'd go catch lizards and snakes and bugs for a while. If my mother had found out she would have died, but this was back when kids still went outside to play and she usually didn't see me between the hours of 9 am and 5 pm, if I wasn't at school.
I remember one particular incident, when some random dog (may have been one of ours, don't remember) stole a lolipop out of my hand when I was about seven. I chased that dog down, tackled him, fished my lolipop out of his mouth, wiped it off on my pants, and went right back to eating it. I was a MAJOR tomboy, and the stuff I did as a little kid was insanely gross. I'm only marginally more civilized as an adult. 
And you know what? I've never, in my life, been seriously ill. I have no major allergies unless you count mild lactose intollerance. As a kid I would get a cold or maybe the flue once a year or so, usually in the fall when all of the kids at school were sick and one of them gave it to me. Even when I did get sick, it always seems to me that it was milder than when the other kids got sick. The kids I went to school with who had super yuppie soccer mom germaphobe parents were CONSTANTLY sick. They had allergies out the wazoo and loved to list all of the things that they COULDN'T eat or COULDN'T come into contact with. Half of them carried hand sanitizer in their pockets. Alot of them wouldn't pet a dog because of "germs." All of them constantly had snotty noses and were wheezing and sneezing and got too sick to come to school at the drop of a hat because they all had no immune systems to speak of.
I wasn't filthy in general- my mom made sure I had scrubbed all of the filth off of myself before bed and before school and that I washed my hands before dinner- but it wasn't a big deal. I got gross during the day- like all kids should, IMO- and then washed up when it was over with. I didn't carry hand sanitizer in my pocket in case, god forbid, I had to touch a doorknob. I just don't think kids should worry about that kind of thing.
My younger sister, who was born after we moved to the suburbs and my mom decided the world needed to be a more sterile place? She's sick all the time. All the time. She also thinks farm animals are "gross" and only grudgingly touches my animals when she comes over. I would hate to constantly obsess over weather or not something I was touching was "germy." I just accept that it is and move on.
I also ate raw cookie dough, as a kid, and licked brownie bowls. I walk around barefooted almost constantly. I feed my dogs raw meat. I haven't died of a dog-related infection, yet, so I'm guessing that I'm not going to. Callie's right. There are too many germaphobes.
Agreed 100%. This is why kids are allergic to the world and constantly sick nowadays. My kids will be raised with a healthy layer of filth coating them and hopefully they won't develop an allergy to air and sunlight like half of the kids my younger sister knows.