I'm a proponent of barefoot activity. In 2009 I developed plantar fasciitis that was pretty bad, and didn't improve with new shoes, OTC orthotics, stretches, or foot strengthening exercises. Out of desperation I tried some Five Finger shoes, and 6 months of pain went away within 2 weeks.
I no longer run in 5fingers (mainly because my last pair started to fall apart and I need to find a store I can try them on in person), but I still do a lot of barefoot, or near barefoot activity. I lift in Xero shoes and spend a lot of time on my feet in them as well at work. Running is usually in a pair of somewhat cushioned cheap Saucony shoes, however I often end each run with at least 1/4 mile on the treadmill in only socks.
All that being said, your doctors may not have been quacks. For example, if you break a bone, you will need to splint/cast it to heal as using it constantly will result in malunion and a lot of pain. However, leaving the cast on too long will result in shielding the bone and muscle from stress, which will make it weaker over time. They key is the right balance. Your docs may have given you only half the solution to your problem (speaking without knowing what exactly was going on).