[ghc]

The public transit system is shaped by natural barriers and landfill, so the weird layout really has nothing to do with neglect (though there's plenty of that too!). The subway system actually covers a large area including Boston and the urban area surrounding it. The commuter rail mostly serves the urban cores of suburban communities outside Boston, so people drive to the commuter rail and then commute by train from there.

Before covid (no idea what the numbers are now) only 40% of people in the Boston metro commuted by car alone, roughly the same share as those who took the commuter rail and subway. 20% of people commuted by car and bike. The share of people who commute by car in the core of Boston is extremely small. At least 50% of roads in the city are single lane and one way. Parking is expensive and scarce. Driving 2 miles (as the crow flies) can easily take an hour, which makes walking pretty competitive as a mode of transit.