I could easily believe that an agency that's been contracting for commuter rail (or whatever) should keep contracting for it unless there's substantial evidence of substantial gains. Change is expensive and stressful. On the other hand, any large organization--any organization that acts like a large organization--can become resistant to change, full of convoluted processes and assumptions, etc.--private or public. If the shareholders or the CEO or the governor or the legislature regularly treat the organization's work as a sideline, a mere tool to make money or gain votes, people inside may get resentful and/or do a bad job, or even do a decent job of the wrong thing. Sometimes a shakeup might actually help, just because it's a change, but it'll work better if it's done by people who have a good understanding of what the organization is for and how it works.
But I don't see that private is automatically better than public, and if I were starting my own state-funded rail system, I'd build up the management infrastructure in-house, like UTA did with Frontrunner.
OT, I've got a plaque on my office wall that says "One must act as if one makes a difference," from my John William Ward fellowship in the summer of 1992--the time I was an intern in the EOTC in a program created in memory of the late corruption fighter.