Not entirely disagreeing with you, though there's a bit of a conspiratorial tone (for lack of a better description) that makes it seem like there's something actually deliberately nefarious behind underinvestment in rail infrastructure. While I'm quite sure that the auto industry and related entities' lobbying is a good part of why things can get bogged down and why there's a lack of funding, I would push back somewhat on the idea that it's necessarily Big Highway that overinflates the cost estimates of rail projects. With respect to the NSRL and a number of other projects around MA lately, the absurd numbers have come directly from the state, and it's fairly obvious where they've come from (e.g. picking a suboptimal NSRL route on Congress Street with an 'optional' second tunnel to get to the proper capacity under the Artery, doubling the costs; see also their rather blatant sandbagging on East-West Rail and Red-Blue). There's no meaningful evidence to suggest that any of that is anything more than Baker and company hating taxes and spending and not caring about the value in these rail projects.
The basic point is that while I agree that transit is not prioritized, I think it has more to do with general public preference (especially outside urban centers) for cars combined with public and institutional distaste for spending (particularly on things "they" won't use, or won't use as much) rather than necessarily resulting from malign influence from road interests (though their lobbying certainly plays a role).