What is the first rule of life in a Japanese domicile? Remove your shoes. Knowing this is the easy part. The hard part is convincing Japanese people that they aren't the most special, clean and unique people on the entire planet and the only ones whose culture embraces shoe removal.
One of my students did a home stay in Arizona during her first trip to the U.S. and told me that she was shocked that her home stay family took off their shoes upon entering their home. She was absolutely incredulous when I told her that my in-laws also required people to remove their shoes upon entering their home as did my one of my aunts and my maternal grandmother. Yes, many Americans do not take off their shoes when entering their homes, but many of them do.
Does taking your shoes off make you a paragon of cleanliness? No, it doesn't make you anything in particular. It could mean you're clean or it could mean you're too lazy to vacuum. It could also mean that you don't have any pets who will track in as much or more dirt than humans (or leave hair everywhere) or that your flooring or carpeting shows dirt more easily than others.
In cases where there is a culture-wide shoe removal tradition (as opposed to individual choices as is the case in the U.S.), racially-determined attention to cleanliness is not the main factor in creating a fastidious culture. The main factors are weather and technological development. People who live in cold weather most of the time are far less likely to adopt the custom of shoe removal as their feet are going to freeze on cold floors without some extra insulation. I'm guessing few indigenous Alaskan peoples were kicking off their mocs to keep the floor clean. They'd rather keep their toes.
In terms of technology, people who don't develop along lines where they live further from the floor are more likely to adopt a custom of shoe removal. The Japanese traditionally sit, sleep, and eat on the floor. When you're that close to the ground all the time, having the cleanest possible floor becomes rather more important than when you're perched quite high above it, especially if you want to keep your blanket, clothes, and matzo mattress (aka futon) from turning black in no time.
Yet, when it comes to the issue of shoe removal, a little shine of smug and superior comes through any time the topic is broached. Every person (from any country) who says he or she has a habit of shoe removal upon entering the home speaks as if they are the pinnacle of clean and sanitary living. There is an undercurrent of 'we invented the unique notion of taking off our shoes out of thin air' or that their culture stands alone as a paragon of shining whiteness and purity for their customs. Okay, that's not exactly true of most Americans who don't give a rat's ass about what other people think of their habits, but I recently encountered someone who said that shoe removal was a "Canadian thing" for cleanliness and comfort. Yes, the Canadians are known throughout the world for their hockey, maple syrup, Mounties and shoe removal upon entering the home.
When I return to the U.S., I probably will take my shoes off at the door all the time because it is a bit cleaner, but I'm not going to be smug about it or put on airs of being closer to God because of it. After all, wiping your shoes off at the door is probably only marginally dirtier than removing them anyway, but I think the notion of wiping your feet is nowhere in the picture when shoe removal is discussed (and the Japanese don't use welcome mats). It's not like people in cultures where shoes are kept on are tracking in half the lawn every time they walk in.