I have rather the feeling that GSR has been mishandling their trains in many respects (a bit too much emphasis on the high-dollar tourist market, for example), but the real issue here is that the train was running something like twice a week for the last few years. I get the point the minister made about lousy ridership, but a twice-a-week train isn't going to be useful to most people, so it isn't a shock the numbers were lousy.
Edit: The subsidy was around A$1.3m...so somewhere vaguely around $1m/yr US. I can't speak to the revenue side of things, but it does seem like the train was somehow managing pretty decent cost recovery for the lousy ridership levels and lack of pax utility involved.