Historical accident, not politics. The NEC is the only part of the national rail system Amtrak actually owns.
Amtrak exists because a giant railroad company that operated most trackage in the North East called Penn Central was going bankrupt. In the early seventies it went to Nixon and said, essentially "We might survive if we can get rid of passenger service. which costs lots of money and isn't covering its costs for us. Hey, whatsay we make passenger service a government program, and then you guys can screw it up even more and close it down after two years? Then we can sell all the track we no longer need, cover our debts, and just do nice profitable freight in future."
(You probably think I'm doing a dig at Amtrak there with the "government program" and "screw it up" bit, but actually, that really was the plan. I'm not kidding. A few years after Amtrak's creation, Louis W. Menk, the then chair of the Burlington Northern, actually blurted it out in public, saying that the government was making a mess of screwing it up. Look it up.)
So, anywho, the other railroads were also invited to join, as most (but not all) were having similar problems. Amtrak was formed. Penn Central went bust anyway.
The bankrupt Penn Central was then reconstituted as Amtrak and Conrail. Amtrak got the NEC. Conrail got the rest. Conrail became amazingly profitable, was privatized, and finally split between CSX and NS. Amtrak has finally gotten the NEC to be profitable over the last few years, though the rest of its passenger service is still technically "loss making". But the non-NEC services suffer from not being under its control. It can't run Acela Express services on CSX tracks, for example, because it would need massive upgrades to lines that Amtrak would barely benefit from.