The minimalist shoes allow the feet to feel the ground and we simply aren't used to that. We don't really need much protection - just a "tread" like the surface of a tyre to protect the skin- the body is well designed to cope with the rest even when our feet are more conditioned since childhood for the comforts of well-shod urban lifestyle.
The feet only function efficiently when we allow them too - by letting them flex and feel the ground uninhibited by thick cushioning and ramped up heels. The autonomous reflexes, muscles, tendons etc. work to our advantage when we give them a chance and they protect us very well.
When we run on ramped up cushioned heels and throw the foot in front of the body to land on the back of the heel, we end up with a shock of between 4 to 7 times the weight of the body that ripples through the bones and joints.
When the foot lands directly below the body, somewhere between the forefoot and the front of the heel, there is no shock. It's obvious that any amount of displacement of the foot ahead of the body will give a proportional percentage of this shock. Even letting the foot creep 1/10th of that short distance ahead a dynamic shock almost equivalent to body weight will be added during the foot-strike. That force is obviously enough to turn a pebble into a pain with minimalist shoes. Pain is there to warn us but the message can easily get confused. The message isn't to change the shoes, it's to learn to run better.
The other major issue that contributes to sharp pains from stones is muscle tension. For musicians it takes many years of playing a musical instrument to even begin to perceive how progress and performance are dramatically inhibited through unconscious tension. We automatically try to overcome problems by using force and in the process develop chronic tension that becomes self defeating - especially as we are not systematically aware of any of it. Feet are very complex, more so than hands, containing 1/3rd of the body's bones, yet most people can't name any of them let alone distinguish what they are doing with them. Tension is clearly going to play a massive role in any running style that has been built on the "power paradigm" of using muscles instead of gravity for propulsion. If a conscious effort is used to relax the foot completely during the footstrike then it flexes to accommodate even sharp stones pretty well. The foot has t least a million years of evolution behind it (slightly more than the Nike shoe company) and if we remove unnecessary tension and inappropriate mechanics then it just gets on with the job of protecting us.
What makes me feel sure about this? Well, it's clear that 40 years of modern running shoe technology development has utterly failed to improve the statistics regarding running injuries. During all that time nobody was looking at how the body worked naturally without shoes. The initial comfort that shoes provide masks the gross mechanical problems that they introduce which are only expressed as overuse injuries that mysteriously appear over time. Something like 60% of all runners will have an injury like this once per year. Sometimes those problems are very painful and very difficult to recover from - as in the case of plantar fasciitis.
Moving over from a messed up Nike running style to a "barefoot" natural style with minimalist running shoes will no doubt always be very tricky and lead to a new set of potential injuries. However, reflecting back on my own transition, though there may have been various issues with unwelcome pain there has never been an actual injury of any kind. Running prior to this was always like steadily working through the manual of running injuries with each classic issue appearing on cue as the previous one cleared up; shin splints, Achilles tendon, knee pain, ililotibial band syndrome (hip), plantar fasciitis, sciatica - prolapsed discs/ surgery, chronic pain in the quadriceps, torn ankle ligaments, pulled hamstring and lots of minor issues.
Sure you can run "barefoot" and do it all badly - but the difference is that you know it instantly, before any chronic injuries develop. Nike comfort running leads to chronic physical problems just like McDonald's comfort eating leads to obesity - it just doesn't seem that way at the time.