Which everyone in the area uses instead of maybe a couple hundred or so.
Yeah, "everyone," all few dozen people who live in an average square mile of Kansas or Nebraska or whatever other Great Plains state you could use. Frankly, if you were being consistent with your argument, you would be arguing against Interstates across the Great Plains, also. Local traffic certainly doesn't justify roads with that kind of engineering standard (ergo cost), and cross-continental cargo traffic could just as well go by rail via piggy-back operations or containerized shipping at much lower cost to the government (after all, the rails are already built). Or even just via U.S. highways, again at lower cost to the government (since the federal government pays much less of the cost of building or maintaining them, and they're built to lower standards than Interstates). But it was felt that the overall benefit of having a nationally-integrated system would outweigh the cost of building a lot of deadweight infrastructure in thinly-populated areas and, lo and behold, it worked out.
You like to object to the idea of high-speed rail with the idea that the government shouldn't be subsidizing anything other than extremely heavily-used infrastructure that goes everywhere in at least the lower 48 (because, H1-H3 aside, it's not like the Interstate system is much use to people in Hawai'i or Alaska). But, also guess what, the U.S. does that
all the time. There are tons of tiny little airports across the country that get federal money even though hardly anyone actually uses them for commercial travel--if you look at the
lists on Wikipedia, for instance, you'll see plenty of airports with less than 36500 enplanements a year, i.e. less than 100 people per day using them on average. There are plenty of dams and canals that have few if any benefits for people across the country as a whole--what good does the
Tennessee-Tombigbee do for someone in Oregon? What good does the
Grand Coulee Dam do for someone in Alabama? And you could go on and on and on in this vein. If your argument was to be consistently applied, the U.S. government would essentially never fund any infrastructure anywhere in the country. Which, sure, you can argue, but you shouldn't really expect anyone else to follow you.
The fact of the matter is that the federal government subsidizes projects that are expected to directly benefit just one area or region of the country all the time, if for no other reason than to scratch everyone's back or, to put it more nobly, that growing the economy anywhere benefits Americans everywhere. There's no reason to think that high-speed rail networks, regional or not, are or should be different.