I'm convinced the people of Japan have some sort of insidious slipper plot. I haven't yet figured out what it is designed to do or how it is supposed to work but here is a synopsis of what traditionally happens.
If you live in Japan and go home you would step into the door entryway, take off your shoes (without getting your feet dirty in the entryway) and step into a pair of slippers. The slippers are worn throughout the lower areas of the house. However if you step up into the rooms that have tatami (straw mats) then you leave your slippers and walk around in your bare or sock feet. As you go back out of the tatami room, you put your slippers back on. When you get to the bathroom you would of course take them off again and step up into the bathroom to brush you teeth or perhaps wash your hands or yes even bathe. Upon exiting the bathroom you again step into your slippers. If suddenly you had to go to the washroom you would hurry over to the small room with the toilet in it (which is separate from the room with the bath in it), remove your slippers BUT slip on another pair of slippers which are in the room with the toilet in it and specifically designed for such a purpose (even to the point of matching the decor). When you are finished in there, you would remove the "toilet" slippers and put the other slippers back on again. Whew! This is normal. A typical foreigner mistake would be to forget to remove the "toilet" slippers upon exiting the room with the toilet in it, and then romping all over the place wearing those slippers, reinforcing the Japanese opinion of how boorish and uncouth North Americans are.
Additionally if you were to visit a castle or go to a smaller church, there are an ample supply of slippers for all visitors at the front door. Again the visitor removes his shoes slips into a nice, comfy, non breathing pair of slippers which of course have been worn by many who have gone before, and you may then enter the castle building or sanctuary area in a refined and dignified manner.
Yes I concur. Bewildering.