And here is a good reference to a list of cities in South Dakota with their populations:
https://en.wikipedia.org/wiki/List_of_cities_in_South_Dakota
Interesting that there is only one city in S. Dakota with a population greater than 100,000 and only 5 with a population greater than 20,000, and the capital is not among them.
The only reasonable hope of serving a city by a train passing through S. Dakota would appear to be Sioux Falls and Aberdeen, and maybe Brookings. The top five cities together have a population of around 350,000. Of them the only line serving Rapid City do not go to anywhere in particular beyond Rapid City, so the onlt way to serve it is with a train that terminates and turns there. That one could also serve Pierre I suppose. But it is doubtful that it will be able to earn its keep, even at a 30% of cost level.