Here's the biggest book I'm aware of on the subject. I'm familiar with the case the author makes but I haven't read the book. I probably should.

This isn't the source I was hoping to find, but it's an article that touches on the economic difference between the privately built and operated Great Northern Railway and it's subsidized competitors.

A general point I'd make about your intuition for planning is that it ignores tradeoffs. Having an optimal transportation network is not the highest end in the world and it's not at all unreasonable to route around things that have higher marginal value than reducing transit times slightly. It's really no different than the case against centrally planning anything else.