What a marvelous discussion. I've only been to Japan once, many years ago, for only two days, and never left Tokyo. That adds up to approximately zero experience in this specific area.
I have, however, been living as an American ex-pat in another nearby Asian country for nearly 3 years. I also lived in a European country for 2 years many moons ago. My perceptions on how people view tourists and foreigners has been evolving for over 25 years.
Language and customs are the issue I believe, not discrimination or xenophobia. I recently moved out into the countryside: when my neighbor found out my language skills (well, in his language, at least) were poor, he said that would be a problem for him. What he really meant (my brother was doing the translation/interpretation for me) was more like "Aw fuck, this is going to be a major pain in the ass living next to you." He's turning out to be a wee bit of a pest, but that's only from my viewpoint:
it's my responsibility as a foreigner to learn the language and customs first, so I can properly communicate my own customs to my neighbors in order that we collectively figure out how to get along.
In contrast, my neighbors back in the big city I'd been in before were exceedingly friendly and accomodating of my language difficulties. In every developed country in the world there are stark differences between rural and urban people, culture, customs, and even language (dialects, cadence, idioms, etc.)
There are also big differences in the kinds of tourists a rural/urban host might accomodate. Many are self-aware, polite, sensitive and curious. And it seems just as many are complete jackasses. I was mugged right outside a hostel in Brussels by some punks. That event turned me off to Brussels, hostels, Belgium and even Belgians to some degree. That's very narrow-minded of me, but it's visceral, limbic, and part of human nature. I could totally understand if rural ryokan owners would avoid trouble by avoiding foreigners based on even one bad experience, or even rumors and heresay.
I've got a friend in the US who's lived for a few years in Osaka, most recently with his wife for a year while DJing. They immersed themselves in the culture, and made many friends of all ages. If they'd gone to the countryside and tried out a ryokan, I'm sure all parties would have had a good time.
I guess I'd side with the owners of the ryokans: send me the nice tourists and their money, but can we please find a way to make the jackasses stay home and watch reality TV?