I guess I just try to keep my bare-footing to places I'm reasonably sure there will be no broken glass - my own yard, and the parks I go to for hiking and trail running and sprinting.
As far as stones and some pretty pointy roots, you just get used to it.
Also, I noticed that after walking down this one particular rocky creek (6" to 2' deep) I like to walk down (while barefoot), my feet muscles were pretty sore for a couple days. The "baby head" rocks really helped to strengthen those muscles even more than just the running around in bare feet did. But after a couple times, my feet were used to it and they weren't sore anymore.
The trails I go on are usually pretty deserted, but I do pass by others occasionally and they make comments sometimes - it's pretty funny - like "Whoa dude! That's crazy!", "You're really brave.", "No shoes huh?", and my favorite, "See mom! HE doesn't have to wear shoes!"
Oh, something else I noticed since traveling barefoot through the woods, and have confirmed the few times I have gone back to using shoes, the animals and birds are way less "skittish". They either don't run/fly away at all or they only do so when I'm much closer to them. Some, I think it's because I end up sneaking up on them (barefoot is so much quieter), but others do see me and just choose not to bolt.