That video is misleading. No, tracking bacteria from your shoes onto the floor does not put you at risk for contracting disease, unless you're in the habit of licking the floor. In fact, these same bacteria are all over the place: on the door knobs, in the sink, on purses, and especially on your keyboard. In fact if you clean your floors on a regular basis, your floor is probably much cleaner than your keyboard regardless of whether you wear shoes in the house.
What actually puts you most at risk of consuming fecal bacteria is mishandling of raw meat, or failing to cook it properly (especially ground meats due to the way they're processed). That's why it's called "food poisoning": it almost always comes from food.
There are legitimate concerns regarding tracking mud, ruining carpets, etc. But spreading bacteria is not really one of them.