Here's an explanation, based on your body's proprioceptive abilities–that is, the way it can communicate up and down all pathways. When you run barefoot, your body precisely engages your vision, your brain, the soles of your feet, and all the muscles, bones, tendons, and supporting structures of your feet and legs. They leap to red alert, and give you a high degree of protection from the varied pressures and forces of running.
On the other hand, when you run in socks, shoes, inserts, midsoles and outsoles, your body's proprioceptive system loses a lot of input. "This has been called 'the perceptual illusion' of running shoes," says Warburton. "With shoes, your body switches off to a degree, and your reaction time decreases."