Pressure and repeated shocks to the joints mostly. They design fancy trabs that take away the pain, but the shock still reverberates up your leg to the knee and hips. Will post some more info later 
There is a lot of info out there on barefoot running and the Pose method, they are very similar as barefoot running forces you to change your running style.
http://birthdayshoes.com/introduction-to-the-pose-method-of-running-posetech-an-introductionThere are plenty of sites advocating barefoot running, but this is a good article from a neutral source,
http://www.runnersworld.com/article/0,7120,s6-240-319--6728-0,00.htmlIt gives the basic reasons behind barefoot running (or forefoot-midfoot striking). Obviously there are drawbacks in the possibility of glass, stones and dog-poo on our roads. I've ran barefoot a few times without much problem though, keep an eye out for the dog-poo and you'll normally be fine over small stones and even glass because you are running much lighter than you would in shoes. However, it is not worth the risk of a small cut and infection, so I run in my 'barefoot shoes' which are basically a 3mm piece of rubber that protects against stones, glass and poo but still gives the feel, control and natural running style of barefoot.
One piece of advice is to build up distances slowly when running properly for the first time. Anything more than 2k or so at first will hurt, because your body is not used to using the muscles naturally. It will take a little time to train the muscles properly, but you will feel the benefit.
Running properly, you will see fewer injuries - particularly to the knees and hips.
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