As a fact, it's true that JSF subsidizes skaters to some extent( which is called "強化費"), but JSF does not officially disclose the amount or detailed usage.
Therefore we need to note that what is reported is merely "according to people familiar with the matter".
Given that, it's hard to show clear evidence or facts, but as a fan who has been living in Japan and who speak Japanese natively, regarding the financial matters I sometimes think there is some gap between thoughts of Japanese fans and that of overseas fans.
I haven't read everything that is going on GS(so many pages to read!) but I think many Japanese fans are not as optimistic as some posts I found here. Media make various speculations about income of skaters but I've never seen the one which says they are paid a lot from the federation. Some media reports the subsidy for the top skaters(特別強化選手) is about 2,400,000 yen/year (roughly 24,000US$). I'm not sure whether this is very accurate but I don't think this is very far from the reality.
http://www.google.co.jp/url?sa=t&rc...f6C3cmClPhTQFXPfF_F5e2A&bvm=bv.66111022,d.dGc
Though it might be easier for Japanese skaters to get sponsors compared to those in other countries, and although skaters themselves don't talk about these things, I think I have to say many Japanese fans are sometimes really worried about skaters who don't have sponsors.
On the bright side, since many Japanese skaters belongs to Kansai uni. or Chukyo uni., they can help skaters with rink fees which accounts considerable part of the cost that skaters need, as those universities have their own ice rinks.
In Yuzuru's case, ANA covers the costs he needs in skating. This contract is estimated to be about 30 million yen, and he has subsidy for JOC Symbol Athlete; 10-20 million yen. It wouldn't make him face with financial difficulty in his training, but considering the costs that figure skaters needs, it doesn't mean he's presently super rich.
http://www.sponichi.co.jp/sports/news/2013/07/02/kiji/K20130702006131680.html
Mao appears in a lot of CMs in winter, and it must bring her decent rewards (though reportedly amature skaters have to share those rewards with JSF) but it doesn't hold true for other skaters. Yuzuru's popularity after Sochi would allow him a lot of income if he will appear in many CMs form now on, but so far he is not on many advertisements, so cannot be compared to Mao.