A long-distance train is more bang for your buck, not less. Many towns aren't on an LD route. For those that are, though, service connecting a town to the rest of the nation daily can be justified by only a relative handful of people boarding daily, where it would definitely
not be for even a "puddle-jumper" aircraft. Stated another way, a plane that would need to make 10 stops to justify operating it would be a wasteful joke, but a train that makes 10 (or 20 or 30 stops over enough distance) is doing exactly what a train is supposed to do.
Amtrak doesn't stop at every little town along its LD routes, to keep from slowing the train unduly. But if Amtrak ran two or three trains daily on each LD route, either:
1) one could be designated as the slower train that makes small-town flag stops, or
2) flag stops could be distributed across the trains by which one is going through an area during decent hours (6am-midnight, or something like that).
The biggest expense of LD trains is equipment, a fleet of cars adequate to run two or three decent-sized trains a day on each LD route. Not cheap, but hardly a budget-buster in the federal budget. Towns can pay for their own stations, whether it be a platform and shelter, a room or two in the old depot (donated by the chamber of commerce or tourism board, even), or a full depot. The other facilities for LD trains (cleaning, maintenance, food) are often shared with corridor trains at terminal cities, and that would be even more true if there were more corridors.
The capital to make a rail line suitable for LD service depends in good part on how fast you want the service to go, and while an LD train shouldn't creep along at 30 or 40 mph for too long, it doesn't need 90 or 110mph trackage throughout to be useful transportation. (Being able to go 90 or 110 mph when an LD train is in corridor territory is very useful, but those capital works would be justified by the corridor trains with faster LD trains being a welcome side-effect.) In my opinion, an LD train needs to be on average as fast as driving the same distance or between the same points
when driving stops are taken into account. One of the principal advantages of a train over driving is that, while trains stop for stations, they don't need to stop for a half-hour to eat or seven hours to sleep. Yes, some people drive with a lead foot and an iron butt, but a service doesn't have to outrace those people to be practical to the traveling public as an average, as most
other people have bladders and stomachs and eyelids that get heavy once a day.
The nation, the government, is not so broke that we can't afford frequent corridor service in the well-populated areas
and a base of LD service to fill in the gaps between those corridors. In my opinion, both are legitimately matters for the federal government, and rules borne out of a fear of "free-loading" like the 750-mile rule, or the suggestion that the feds shouldn't spend money on trains that don't cross state lines, are short-sighted. States willing to pay more for more than a base level of service should get it, but the ability of an American taxpayer to get to Houston, or Nashville, or Phoenix by some base level of service should not be wholly dependent on the will of state officials or barred by the ideology or ignorance of the same.