Man, I wish people would walk around everywhere without shoes lol... Yes, nail and derm problems may lessen, but if you think we see foot lacerations, trauma, infections now, just wait.
There's no doubt that shoes support the foot and take some work off the muscles, but keep in mind that the main function of covering the feet: protection. It's probably a good idea to walk around barefoot at home to stretch and strengthen the muscles, improve balance, and air out the skin/nails. However, it's just not practical to walk around everywhere with no shoes or shoes that lack support.
As for shoes being what ruined the structure of human feet, I don't think that's accurate at all. Calcaneus density would indicate that people were probably walking with heel-to-toe ("cow," according to the author) gait long before modern shoes were around. The ball-to-heel ("fox") steps might protect somewhat, but they are much slower and less efficient. Wearing shoes doesn't have to mean bad feet, but wearing ill-fitting shoes or wearing shoes all the time probably will have those effects.
It's a decent read, but it's just a lot of speculation and anecdotal evidence.
Also, let's consider the practicality... and the source
:
http://anthropik.com/author/jason (<- basically says "computer nerd with no anat/phys training")