I have never been to Boston, but if this is true then why is the public transport map so weird? There's the subway for inter-city travel but if you're commuting then commuter rail does not seem practical at all because of this weird gap? To me it made the impression of a neglected system, presumably because everyone commutes by car. Is there still space downtown for e.g. bicycle lanes? Otherwise this surely would have been fixed for decades now.
Or is it just painful to commute because there's a livable downtown with public transit, bike lanes etc., which was not completely sacrificed for cars, but just without a great commuter solution?