Did you miss this paragraph? They do talk about the subsidies from the national and prefectural governments.

> Carefully designed public subsidies also play a useful role. Although Japanese railways do not receive subsidies for day-to-day operations, they do receive government loans and grants for capital investments. These are typically tied to public priorities, such as disability access or earthquake-proofing, or to projects that have large spillovers that the railway company would be unable to internalize, like removing level crossings, or elevating at-grade railways or trams in order to reduce road congestion and accident risk. Generally, the local prefectural government will match the contribution of the national government. Larger new build projects are subject to lease back or debt-payment conditions that fare revenue is expected to pay back.

Unless this was added after the fact, I think this is mostly an issue of careful reading. To me, the article absolutely says that it's a hybridized system like you mention.