Much can be done with creative accounting to make the numbers sing whatever song the composer wants.
Are all the crew costs assigned to the one train, or are they spread among several if the crews operate on other trains. Station costs....all on a train or a couple trains daily, or against a region or system. Track charges by the freight lines, equipment and so on.
When passenger service was provided by the RR's, so many costs were charged against passenger traffic with the aim to flooding the ICC with red ink.
Like most public transportation, the fare box hopefully covers the fuel and labor of the trip. Subsidy covers the equipment, maintenance, and management.
When these "tales" appear, the response should be: imagine if the airlines built their own terminals, runways and footed the bill for air traffic control.