I don’t see where the federal government has any business funding local transportation systems. But Amtrak, quite simply, is necessary for national security reasons. We cannot be wholly dependent on flight for medium to long distance travel, and personal vehicles have serious limitations in emergency situations.
If you don’t see how this is a national security issue, I refer you to the events of 9/11. I was in NYC on 9/11, and the Amtrak service through NYC was one of the major hubs for handling the massive number of people stranded hundreds or thousands of miles from their homes when air travel ground to a sudden and complete halt and dropped them off at whatever airport was closest when the universal order to land went out. I bumped into US citizens who’d been stranded in Canada on their way home from business or personal trips to Europe, using Amtrak as part of their makeshift route home to distant parts of the country. Even after air travel began to resume, it was several days before airlines could get their planes back to the right locations from which to offer reasonably normal service, and the NYC Amtrak station remained extremely overloaded for at least two weeks after 9/11. Without Amtrak to fan these stranded hordes out across the country, to places where they could pick up rental cars, regional bus and rail service, be picked up by friends and relatives, etc., the chaos and economic damage would have been much greater.