I don't know if Usagi Drop is a great example to use. This may be very naive of me, but presumably the fact that the ratings for noitaminA are probably double (if not more) of the average SHAFT show means that advertisers pay more to Fuji TV in the first instance to show commercials during Usagi Drop's broadcast.
I don't know who it is that needs to make money on the show for it to be considered a success - the TV station, the production team, or the licensors of the Usagi Drop IP (the publishers most likely, although I don't know how manga licensing works and whether anime rights remain with the original mangaka?). But someone somewhere is still managing to find money to fund these shows, however diminished noitaminA's star may seem at present - and even bearing that in mind, despite how disappointing 2011 was most of the shows had decent production values and didn't come across as "cheap".
I think I've kind of forgotten my point, but basically what I think it is is that a noitaminA show possibly doesn't make mounds of money I wouldn't necessarily see poor disc sales as being an indicator of the show failing financially (and certainly not critically). Hunter X Hunter 2011 hasn't even sold a Fractale, and I don't think anyone would call that a failure.