The New York Times' report on the exorbitantly overpriced Second Avenue Subway work highlighted extensive union featherbedding in that instance, which probably explains some (but not all) of the cost premium.
Another plausible factor is the push to privatization and contracting in the US public sector removing effective management from the picture, so that the public sector is no longer capable of cost control. For example, by realizing when bidders on contracts are bullshitting too high or too low, or by pushing people to suggest cheaper designs.
A corollary to the previous point is that the US generally seems unwilling to look at foreign countries (especially countries not named Canada or the UK) for insights into what can be done better. This can result in people not adopting newer, cheaper technologies in a kind of NIH syndrome.
Another possible factor is that, for several kinds of projects, the US's diverging rules (e.g., FRA regulations basically banning all European rolling stock until they were revised a year or two ago) combined with a relatively low install base could be preventing economies of scale to make things cheaper.
There's lots of plausible factors. Actually digging into what makes them so expensive is very time-consuming, and I suspect there is very little pressure (let alone ability!) from anyone on any side of the political spectrum to actually make it happen. It's much easier to pick the factor you personally believe in and say it's so without any evidence to back it up.