They do. The northeast corridor (where the accident happened) *does* operate in the black (as does the Empire Corridor in NYS and I believe the pacific coast trains). However, the routes connecting all of these regions lose a lot of money, and have more senators along the way.
There are two reasons we have Amtrak: One is the intentional destruction of local transportation infrastructure caused by the likes of GM, Greyhound and Standard Oil, from the 30s-50s. The other is that the government in the 60s was heavily taxing railway tickets and infrastructure and directly funneling the funds into airports and interstates, the very competition of the railroads. They were taking rail stations, moving them out of downtowns onto freight bypass routes on the outskirts of towns, and putting highways over the old ROWs. Passenger rail became unprofitable, but the companies were being forced to continue running the unprofitable passenger services by regulations. The result was they started going bankrupt. By the time the government realized the national rail infrastructure was about to disappear like a fart in the wind, they hacked together Amtrak as a way to "bail out" the railroads from a problem largely caused by the decades of meddling.
Tl;dr: unfair practices by both the private and public sector killed profitable passenger rail half a century ago, and no one knows how to fix it. Amtrak is the band-aid.