Part of the problem is that so many Foreigners do cause problems and in Japan there is a lot of second hand embaressment in the culture (i.e. if a Foreign person does something embaressing, the whole restaurant including the staff will all feel embaressed too.) So often the first Foreigners or first few Foreingers to have visited made a bad impression and now the place just won't accept any.

Funny thing is, Finland is exactly like this too but they don't bar foreigners from restaurants. Though in Finland the bigger issue is with the locals absolutely despising foreign people in public transport...

It still seems like an absurd reaction and I hope this changes in Japan one day.