I often go barefoot to rock climb (warming up), on short hikes, running around the house, doing yardwork, etc., and have some pretty tough soles...but I still cringe at the thought of scree and talus fields and what my feet would look like after a thru-hike...One misplaced step and oops, there goes the big toenail...
I think it all depends on where and why you're going barefoot.
Going barefoot obviously goes WAY back into human history, but then again so does footwear, depending on the region and the needs of the culture. Early humans braving Northern European winters without footwear...don't think so.
I'm a runner and do believe that running barefoot is probably fine, maybe even good for you- ON THE PROPER SURFACES. Bare human feet didn't evolve on asphalt and concrete; any runner knows how potentially destructive these surfaces can be.
Knowing that millions upon millions of humans have lived their entire lives barefoot, I'm tempted to believe it's more "natural", but then again, when have you ever seen data on how common major foot problems, lacerations, broken toes, fractured heels, etc. are in these societies? I've been going pretty hard for 30+ years without a major foot injury. Is it luck or shoes?
I'll take a lightweight pair of street running shoes with plenty of mesh for my journies (3 season)- to me, they're the best of both worlds.