Whether the Northeast corridor is entirely or primarily owned by Amtrak is inconsequential.
The MBTA is a transit line. It's also in the Northeast Corridor, which, as I've already established, is quite different than the majority of the country. I assume you are from the northeast, so I understand your confusion regarding the status of Amtrak in the rest of the nation. In the majority of the country, Amtrak travels on rails owned by the railroads, and the railroads are very much not fond of passenger rail. They are forced to provide access to Amtrak as part of the agreement that allowed them to discontinue revenue passenger service. The railroads were obligated to provide revenue passenger service as part of a bail out in teh early 20th century.
I read your link and it literally has no bearing on anything I just said, because of the aforementioned fact that it is in the Northeast Corridor. Furthermore the agreement was signed in 2003, which has nothing to do with anything I am talking about. Third, the Northeast sucks for rail freight because the loading gauge is so small compared to the rest of the country, and population density is higher, so passenger rail is comparatively better there than elsewhere.
Your superior knowledge on the subject is merely illusory. I suggest you do some research into the history of passenger rail in the United States. I'm sure you are intelligent, but your attitude sucks. Here's some stuff to get you going:
https://en.wikipedia.org/wiki/List_of_railroads_eligible_to_...
http://www.aei.org/wp-content/uploads/2014/03/-hiltonamtrack... (warning, pdf)
Railroads took Amtrak to court over passenger rail scheduling (this article also gives a bit of a rundown of the conflict):
http://www.eenews.net/stories/1060008220