I'm rather amused by the offense some seem to be taking to the suggestion that wearing shoes in the house is filthy, especially given the article that this discussion is about.

Yes, it is disgusting. Why is this a question. Better: why are we pretending this is a question?

Much if not most of the world takes their shoes off when entering a house. It's not just the Japanese. It is the practice in Northern/Central/Eastern Europe, the Middle East, Ethiopia, India, etc. Besides, taking your shoes off allows your feet to relax instead of being cooped up inside a small, confined space for all your waking hours.