I've had a number of people complain about my lack of shoes in my research building. The complaints come from the other departments that occupy the building as they don't know who I am and so just see some weirdo walking around without shoes and socks on while my department understands me as being a barefoot geek. This has been going on for some weeks and I've recently been found by the local health and safety wardens who have alerted me to the complaints and said I should not be doing it.
Their reasons go along the lines of 'what if someone leaves a drawing pin on the floor' or 'the floor in the toilet is dirty you can't possibly walk in there'. I said I'd put some slippers on which they seemed to accept. However, what I later realized is that theses folks who are complaining don't realize I'm barefoot all the time. They think I come to work, remove my footwear and start wondering the halls. This explains their worry that i might step on something as they don't realize I have to navigate the gauntlet of the outside just to get to work, so floors indoor are no real challenge to me.
As for using the toilet. Yes the floor is covered in nast, but that's life (or more accurately the poor toilet habits of many shod men). I take special care, unlike outside, to not enjoy any puddles I find in the toilet. And the next time I get told off I'll just ask them if they use the toilet door handle when leaving the facilities - as there is probably more germs on that one item than the whole of the floor (which is cleaned daily). By the way, I avoid using toilet door handles where ever possible.