Running barefoot has historically caused a lot of issues. Aside from the obvious possibility of stepping on something in the environment and developing an infection, the grounds we walk these days are not forgiving. Walking and running barefoot after completing adolescence causes undue stress and pressure to the feet. This can lead to tendinitis, bone contusions and stress fractures (just to name a few). Even minimalist shoes that were once thought to be the optimal way to run have been debugged. 

The shoe type that is right for you is in some ways determined by your foot structure, but even with this taken into account, minimalist shoes add up to being not worth the risk.