But I can't help but feel that this author wants to dislike trains. He wants everyone to understand how awful and slow it is. And they went into this story with a chip on their shoulder, and were disappointed to find that the trip had value.
But the trains aren't just about cross-country travel. They travel through small towns where people rely on them for trips to larger cities. If you live in Mount Pleasant, IA, you can take the train into Chicago just as fast, and far easier, than driving. Want to go from Salt Lake to Denver in a blizzard? Trains will take twice as long as driving but you can sit there and safely watch snow-capped peaks go by instead of worrying about driving your car off the edge of a mountainside. Pick any 2-6 hours train trip on the map, and those are the majority of passengers on Amtrak. And I have frequently run into retired people heading to Iowa to pick up RVs, because Winnebago contracts delivery of RVs out, and it is a nice part-time job to get a one-way train ticket, then drive a RV to someone's home and get paid for it all.
In short, the purposes serve by Amtrak have as much variety as reasons people get in their cars. It is a valuable service to those who need it, even if authors for the NY times aren't the 'target audience'.