The no fly list could be a topic on it's own, but that would stray so far from trains as to not belong on the site at all. While I thought the creation of the do not fly list was a good idea, and it has for the most part achieved it's goal, there have been quite a few interesting stories out there about people who find themselves on the list, are never told they are on the list until they arrive at an airport, and don't know why they are on the list. There also (from what I have read) is no formal appeals process to get off the list if there has been a mistake. So there is little if any due process involved.
I have a couple of issues with Amtrak being part of this list. First would be, as someone else mentioned, it was created as part of an aviation security act, and Amtrak is not involved in aviation. I suppose there could be some sort of amendment, but one has to wonder to what end? Is there some chance that anyone could hijack a train and take it off track and into a building? The purpose of the list does not seem to jive with the mission of a railroad. Second of course would be list criteria, which is still a state secret, but if you would be added to a list of terrorists because you didn't wear a mask in public, then we have already gone too far down that slippery slope. Third, while preventing movement of terrorists is a noble effort, the primary transportation method used by people in this country is still automobiles. Adding a railroad to the no fly list does nothing to stop a road trip of epic proportions and I would say that a car bomb is a much more prevalent threat than a train bomb, which I have never even heard of.
Now can Amtrak come up with reasonable mask rules, sure if they want to. Just like the restaurant rules that recognize you can't easily eat with a mask on and have adapted. Although I find that adaptation to be unscientific no matter which side of the mask debate you come down on, it is still an adaptation made for a specific purpose. Amtrak could do the same if they wanted to. I suspect that whoever at DOT wrote the rule for trains, may never have been on one, and may not know there are private rooms. This is an area where passenger advocates could get involved in advising the railroad.