WCR is a private company, true. But they are contracted by the government
to operate a passenger service for the Ministry of Transport. All ticket
revenue goes to the government, who then pays the contractor a standard
fee per passenger journey. It is still a GOVERNMENT service, but operated
by a private contractor. It is NOT a private railway. Just like most (now
all) suburban buses.
Hoys is another contractor which operates the Shepparton service for the
MoT. The difference with Hoys is that they chose to hire rollingstock from
V/Line rather than owning it themselves.
V/Line Passenger is also contracted by the MoT to rovide the remainder
of public passenger services.
Cheers
David