I've been wearing Vibram Five Fingers and running on the fore- and mid-foot for about two years.
Running barefoot and landing on your heel jars your entire body (knees in particular) and isn't sustainable for long distances. Cavemen certainly didn't run this way, and we haven't evolved fast enough for our optimal mechanism to be any different.
There's plenty of evidence that humans have evolved to be better long-distance runners than any other animal. The amount of impact energy returned by our tendons is highest, and human ultrarunners can go over 50 miles in one sitting.
For a couple weeks, my calves screamed and my feet were sore as they strengthened. Then after a month I started to get used to running on the balls of my feet. After two months, I felt totally comfortable with the new style.
Also, my trouble with Illiotibial Band Syndrome disappeared within two weeks of starting to run barefoot.