The example of going from Newton to Harvard is that you would have to cut through Boston via Storrow/ Soldiers Field Rd. The larger point is that there is little connectivity in a hub and spoke system. Brighton to the Seaport, Hyde Park to Longwood, etc. You have to drive.
I respect people mentioning bus service, but after 30 years of riding the system I can tell you the busses are terrible. Not by design, but they have to travel the same congested and narrow streets, they're overcrowded and the schedule is unreliable especially if you have to make a connection or be somewhere by a certain time. This is why subways exist, to get people off the street grid. I have little faith that ithe bus system can handle extra volume.
Finally, all of these proposals aren't taking reality into account. They all assume voters have no recourse to oppose yet another tax with a questionable benefit (more T employees, pension payments, bus drivers now make 50 bucks a hour, or does it actually go to improvements). A huge trove of people that live in the suburbs will get hit with this cost. They will immediately put a referendum on the ballot to repeal, especially since some of you plan on charging patients who drive into city hospitals for treatment. That should go over real well in a campaign ad.