Earlier, I'd dredged up Amtrak's costs per train-mile in an effort to see the breakdowns in expense for each route. Unfortunately, it's a touch out of context being composed solely of American routes. We can see that some routes are rather more expensive than others, and others apparently being absurdly cheap, but the major question of whether Amtrak's costs are reasonable is unanswered. For comparison purposes, let's look at the Japanese railways.
According to JR Central's 2005 annual report (page 60), they ran a total of 94,273,000 train kilometers in that fiscal year. Against this, page 3 reports $7,605,074,000 in operating costs and expenses for the railway sector of their business, which comes to a total of $80.67 per train-kilometer or $129.83 per train-mile. Adjusting for inflation, from 2005-2011 dollars, it comes out to $150 even.
For JR East, using Central's reported figures, they ran 259,594,000 train-kilometers on an expense of 1,677,929,000,000 yen (page 15), or $15,681,579,439 at the applicable 107:1 exchange rate, producing an operating expense of $60.41 per train-kilometer, $97.22 per train-mile, and $112 adjusted for inflation.
With JR West, again using Central's reported train-kilometers figures, we have 199,796,000 train kilometers on $8,225 million in transportation operating costs. This equates to $41.17 per train-km, $66.26 per mile, and $76.30 after adjusting for inflation.
As it turns out, Amtrak is actually in decent ground when it comes to expenses per train-mile, thought it must be kept in mind that these numbers do include a large amount of commuter work, which should have lower expenses. Where the problem lies is in the fact that the trains are so small, raising the costs per seat-mile and rendering them unprofitable as a result. It's actually rather puzzling why Amtrak chose to build the world's smallest passenger capacity high speed rail train especially at a time when both Japan and France were building double deckers to add even more seats and capacity to their future trains.