My preference when weather, surface, and activity allow is to be barefoot. Next preference are Vibram 5-Fingers, which allow natural mechanical function, while providing some protection. For work (my job) and for some projects at home, boots are a necessary protection.
Like others have mentioned, our feet are made for walking and running. I used to have frequent "ankle rolls" in boots or shoes. Too many places I went required more protection than bare feet. When I started wearing the 5-Fingers, I found that my feet, ankles, and lower legs developed more strength, flexibility, and stability. And, it's harder to roll an ankle without a clunky shoe/boot heel or sole in the way.
Flip-flops are good for some situations, but not a good full-time option. I wear them when I'm planning to spend time barefoot, but need to get past areas that aren't good for bare feet. They're not safe for climbing on anything, or for walking on rugged terrain. And, of course, they don't lend themselves to normal foot mechanics, as they require some effort to keep from walking out of them.
At home, I use two pairs of Crocs...one for the front door and one for the back door. If it's a quick trip outside, I can slip into them, keep my feet clean and dry, then I ditch them outside the door and go back into the house barefoot without tracking dirt or mud inside. Or, if I'm spending lots of time barefoot outside, I can easily wash my feet at the hydrant, slip into the Crocs, and walk to the door with clean feet. They provide a little protection, but also a false sense of security. I recently stepped on a cut-off pine sapling stump with Crocs. I'd cut the area with my brush mower, which creates something like a pungee stick...sharp pointed and well-rooted...that takes a while to decompose. The rubber Croc kept me from feeling the sharp point before I put weight on it. Not feeling the point, I continued my stride. The rubber held until there was sufficient weight and force to drive the point through the rubber, through the bottom of my big toe, under the skin, and out through the top of the toe. I'm pretty certain that if I'd been barefoot, I'd have felt the point and instinctively corrected my step, avoiding injury. Even if I had gotten "poked", I wouldn't have put my full weight down, so it wouldn't likely have been a "through-and-through" injury.
Someone mentioned snakes. We have lots of snakes in Arkansas. Most are non-venomous, but we do have a few different species of rattlesnakes, "Cottonmouths" or water moccasins, and copperheads. There are frequent warnings about snakebites and bare feet. But most snakes, and particularly the larger rattlesnakes and moccasins, are usually going to strike higher up, somewhere in the calf range. Copperheads have been known to bite toes, but they're usually trying for something higher, too. Like mentioned in another post, bare footing requires a level of attention to where we step, which helps to keep aware of snakes.
On the subject of natural foot function, I'd recommend reading (or listening to) Christopher McDougal's book "Born To Run".
