A political reason is that the keep-Amtrak-alive coalition is basically a mixture of urban transit advocates and representatives from rural areas who want to keep their town's train stop. A system that only served the major cities wouldn't have broad enough support, especially if it were only the major coastal cities (e.g. if you cut the Chicago, St. Louis, Pittsburgh, etc. services).
A political reason is that the keep-Amtrak-alive coalition is basically a mixture of urban transit advocates and representatives from rural areas who want to keep their town's train stop. A system that only served the major cities wouldn't have broad enough support, especially if it were only the major coastal cities (e.g. if you cut the Chicago, St. Louis, Pittsburgh, etc. services).