I’m not sure why nobody has brought this up, but if you are riding in coach, talking to strangers, starting your trip in crowded NYP, and going through states out west where people are not social distancing or wearing masks, and possibly screaming in your face because you are wearing one, you are much, much more likely to get sick from the virus than attacked on Amtrak.
My nearest station—TRE—is, unfortunately, one of the creepiest in the network, but even there I do not feel unsafe. I go down to the platform, where the passengers are, instead of waiting in the station, where the vagrants live. And of course never go there at night. (I am a 5’1” woman and, one plus of being in my 60s is that nobody notices me!
.)
To be safer from the virus, I would suggest springing for a roomette when possible, not talking to anyone except the SCA or conductor, staying 6 feet away from everyone, and not getting out for breaks when the train stops in states where people are not wearing masks or social distancing.
Also, is there any way you can leave from somewhere less crowded than NYP? Even though people in New York seem to be trying to do the right thing, it is still a crowded city and probably impossible to keep a 6-foot distance from everyone. (For example, I am planning a tentative trip from NJ to NYS in October and am going up through New England and out through Boston so I do not have to be in NYP.)