This is in danger of turning into another tablecloth/eating in supermarkets thread...
The hygiene hypothesis isn't my theory, it's a theory espoused by leading allergy specialists seeking to explain the huge explosion in allergies in western, developed countries over the past 30 years (and the UK is worst of all). Doesn't really have anything to do with shoes off policy, though, as it wouldn't create a large enough effect. The point I was trying to make is that people who go 'yuck' about other people wearing shoes indoors 'because it's dirty', even if there's no dog mess/muddy shoe issue, are working on the same principle that may be responsible for the rise in allergies ie dirt is a bad thing and must be completely eradicated hence the market for anti-bacterial wipes (which are a complete waste of money, BTW, but that's another story).
Obviously if you live on a farm you take your shoes off, so does every farmer I know. But children who grow up on farms are still exposed to many more (thousands of times) infectious agents than urban children, despite the fact that farming families generally keep VERY tidy and clean houses ? it's just the environment and it's a good thing, because it protects against allergies.
And the cultural differences about shoe-wearing between Eastern and Western countries doesn't mean Eastern countries would have more allergies, because there are many, many far bigger factors. Maybe it's like the Japanese diet, though; people in Japan are far less prone to heart disease but Japanese people in Western countries who eat a Western diet have exactly the same heart attack risk as everyone else in those countries. So it clearly isn't genetic, it's environmental, hence the idea that it must be a dietary issue.
I guess north/south cultural differences about this habit may come into play though. Maybe I think it's rude because I'm a northerner. Still think it is, though!