The BART extension was a gold-plated addition to a custom-all-the-way system, but that was necessary politically and to minimize impacts on San Bruno along the way (subways are expensive - witness the current Chinatown thing in SF -- almost $1B/mile for "light rail" that's usually $10-40 million/mile including stations and wiring). BART simply can't be built for $4-5m/mile like a freight railroad. Not to say some of the gold plating couldn't be dropped, but cramming a high-standard transit line into an existing urban area where the only previous track was a long-unused single-track spur line isn't cheap.

Our classic in Sacto was the "Gold Line" and "Blue Line" projects. "Gold Line" extensions (several phases) from Butterfield to Folsom cost around $10-20m/mile including stations, electrification, and a couple of bridges - using r/w they already owned and moving the only-occasionally-used freight spur over for space. But when they did the Amtrak extension part of it downtown, in streets in an old downtown area where not much is known about very old utilities and archaeological stuff, there were all kinds of discoveries and delays and cost zoomed past $40m/mile. "Blue Line" was in between - high $20's/mile - but it involved buying (condemning in spots) r/w and moving a UP main line for space. Many Big City light rail systems even (not BART) would kill for costs that low - a benefit of being in the boonies I guess. Then there's inflation - all the bills aren't in yet but I suspect the new "Green Line" to the river will probably come in around the $40m/mile range, and the Blue Line extension now starting construction even a bit higher due to the structures needed. Costs go up as the years go by.

And if you've dealt with UP from the outside, you'd find that they're not skimping on charging others (mainly the State) pretty fat prices for work they do on "capacity expansions." $4m/mile track generally isn't for passengers.