We started reading about natural hoof care and "barefoot" riding several years ago. One of our first sources was The Natural Horse: Foundations for Natural Horsemanship by Jaime Jackson. Jackson's theory is that mustangs go barefoot over incredibly rocky territory in the mountain west, and they seem to do fine. In fact, when their hooves are studied (usually after death, because nobody's picking up the feet of a range mustang!), the hoof walls are beautifully self-trimmed. This Wikipedia article http://en.wikipedia.org/wiki/Jaime_Jackson talks about Jaime Jackson, a man who researched wild mustangs in the Great Basin (where we live) and found that they have far less hoof problems (navicular syndrome and laminitis) than domestic horses. He started a movement toward natural hoof care that is growing in popularity.
At first we were skeptical that horses could be ridden safely over rocks without shoes, but we did more reading on how to trim the hooves correctly. The correct trim, as illustrated in Horse Owners Guide to Natural Hoof Care, again by Jaime Jackson, is shorter than the usual trim for shoeing, and with a "mustang roll" around the outer hoof wall to prevent chipping.
Through reading Jackson's work, and also Making Natural Hoof Care Work for You by Pete Ramey, which has a lot of "work in progress" photos of trimming techniques, we learned to do our own hoof care. As we spent more and more time riding barefoot, we found that the soles toughen up, the hoof walls strengthen, and the horses seem comfortable going over all kinds of rocks.
At the beginning of the spring riding season, our horses are long in the toe, but we trim them back as work over rocks causes the sole to scoop out into its concave natural shape. After a few weeks of steady riding and trimming, the hoofs look better and better.
For horses ridden infrequently without adequate time to toughen up, no doubt using protection (iron shoes or rubber boots) is the best bet. Or, for horses ridden more than the 50-70 miles per week that our horses usually go, protection might be necessary to prevent the hooves being worn down too much and cause them to be tender for that reason.
We're amateurs at this and still learning, but so far going barefoot (with those rare exceptions when we need boots for extreme rocks) seems to be working out very well.