I wonder if these high costs are due to it being passenger rail inside a major city. I'm curious if this cost applies to freight rail as well.

Out here in the countryside it seems that a mile of freight rail should be worth much less than a mile of highway. Everything from easement size to site prep, equipment needed and bill of materials seems a fraction of that required for highway construction.

As mentioned elsewhere the maintenance is minimal compared to a highway as well, with the trains plowing snow themselves and the rails being very hard-wearing. The only work we ever see them doing on the rail lines is occasionally replacing sleepers and fixing up the road crossings - and it's heavy trucks that ruin those, not the trains.