On the contrary. These were not isolated incidents. Violations were widespread in their hotels across the entire country. This stemmed from head office policy.

[EDITED TO ADD: There were violations at 60 of the chain's 122 hotels, according to Japan Times: http://search.japantimes.co.jp/cgi-b...060207a1.html]
In addition to those 60, 18 hotels were illegally altered to violate regulations on disabled access:
http://en.wikipedia.org/wiki/Toyoko_Inn
IIRC, experts explained at the time that the violations could have trapped people in the event of a fire.]

It's also true that the hotel won't let two men share a double. (Two women, or a man and a woman = OK).

The hotel hates gay people and handicapped people - as evidenced by its policies. But, whatever. Why should able-bodied straight people care? (Sarcasm alert)

The best I can say about this is that there are doubtless other hotels in Japan that have committed similar offenses without being caught. However, Toyoko stands out for really driving this cr@p from the headquarters level. AFAIK, the company hasn't changed it's fundamental character since this incident. You can find more recent complaints on Debito's site and others.