Since around 1950, most short lines have been created from "marginal" branch lines formerly operated by the major rail carriers. That is, selling off the lines to a smaller operator would allow a reduction in expenses, (particularly for labor, since some of the cost structures formerly mandated in the major road's contract would no longer apply) but also might allow for more direct contact between carrier and shipper, improving the quality of service.
But over the years, a number of family-centered corporations (Robey, Corman, and Salzberg come immediately to mind) gained control of several of these lines and estblished uniform operating and managerial procedures. Some of these lines also deal extensively in the equipment-lease market.
It's worth noting that the size and overall capacity of short line operations has been growing as larger parcels of property were "farmed out" by the major roads. Also, that carload traffic of low-valued freight which is not sensitive to time constraints shows signs of recovering after many years of decline/dormancy.
Some of the most prominent business success stories of recent times have evolved not from capital-intensive centralized planning, but from the grouping together of cast-off, "hard to fit" entreprenurial opportunities. One of these days, a couple of short lines might be able to string together a service which relieves some of the pressure on our congested freight lines, and at a reasonable cost. That would be a red-letter day in the history of the rail industry.
I wouldn't count on setting up a short-line by the same rules as a retail franchise, however.
Here's another thread which conveys some of the issues involved: