Walking barefoot seems like such a natural thing to do, and that may have been the case tens of thousands of years ago. But there's a reason your ancestors started wearing shoes, and it wasn't solely to keep their feet warm. The shoes protected them from various ailments and injuries. Even today, walking barefoot too much can create problems for your feet.
When you walk barefoot, you're not giving the arch in your foot any support at all. Even if you have low arches, your foot can react to not having a cushion underneath the arch. In the past, when your ancestors roamed around barefoot, they walked on dirt and grass that let their heels and the balls of their feet sink a tiny bit into the ground with each step. On hard floors nowadays, you don't have that sinking, and it places pressure on the rest of your foot, stretching the arch unnaturally and making it easier for your foot to roll inward, or overpronate. Overpronation can lead to ankle injuries. Carpet isn't much help either (though it's certainly better than hard flooring) because it can be too soft and not provide any support.
The connection between the fascia at the bottom of the foot and the heel is rather sensitive and can become inflamed easily. This can bring about a condition called plantar fasciitis if you don't protect the area. Plantar fasciitis is not a permanent condition, but it can feel horrible while you have it. Running in unsupportive shoes, dancing barefoot, and a host of other activities up your risk factor for developing the condition. Stretching the fascia with a tennis ball or frozen bottle can help alleviate some of the pain.
Plantar Warts and Other Creatures
Your shoes and socks not only cushion your feet but act as a barrier toward pathogens. Walk barefoot, and you can pick up undesirables such as the virus that causes plantar warts or various fungi. While healthy feet might not develop much of a problem from these, if you have even a tiny cut or scrape on your feet -- which can happen without you knowing -- the pathogens could enter your body.
If you've been dealing with foot problems for a while and would like some help treating them, contact a podiatrist like http://www.advancedfootclinic.org or sports doctor. Foot conditions can usually be soothed quickly, if not healed quickly, and the sooner you have someone look at your foot, the better.