It's not billions. More in the neighborhood of $300m - $400m per year. The answer is difficult, but largely political.

Amtrak is without a doubt perennially losing money, and lots of it. They make a profit on the heavily travelled northeast corridor but lose much more on almost every long distance route. Many of these routes serve small towns with no other connection to major cities (except roads, but no bus service). In that way, it is similar to essential air service. Many of these towns lobby for continued service, and since the government is subsidizing Amtrak they are more likely to continue to do so; they lose incentive to turn a profit. The town wins, Amtrak sorta wins, most taxpayers lose. Very similar story played out all the time in govt.