People in Japan not only take their shoes off at home, but also in many other places as well. Most elementary schools and many doctors offices, eye doctors, etc.. have you take your shoes off, although it varies from place to place. Some restaurants require you to take your shoes off. I once visited a radio station and they took their shoes off there too for some reason (no, I don't believe it was ESD related).

So people are already doing this multiple times a day at their own homes and form a habit that often doesn't require much thought to follow.