Something I have learned from my podiatrist.... As an instructor, I am bouncing around and pounding on my feet regularly, my poor feet have had stress fractures and other problems. My podiatrist gave me a few tips to help my feet stay healthy.
1) flip flops are the worst possible shoes you can wear on your feet so STOP it.
2) put some sort of orthotic or over the counter insole in your workout shoes. The insoles that come in your shoes are extremely thin and not supportive. It will also help with the longevity of your shoe.
3) you should NEVER be barefoot. (Even if you are just walking to your bathroom in the middle of the night). The recommended shoe... CROCS! I know, it is the ugliest shoe known to man however, it is the most comfortable shoe ever! Once I finally got past how ugly they are, they truly became my best friend. I also have become extremely used to having shoes on my feet always. It keeps the feet from getting dry, supports the arches, and cushions the padding of your feet. I hate being barefoot now! Give it a try! You will love it!