Distance-bsaed fares make sense for longer radial trips (i.e. outside 128). For the urban core (i.e. up to 128 or so) with a wider variety of trips, I would argue that a flat time-based fare would be better. Unlimited transfers in 90 or 120 minutes. Again, treating transit as a public good to maximize mobility.
Distance based fares could still make some sense inside the 128 beltway. With so much talk of extending the Blue Line to Salem and Charles MGH, does it really make sense for a Blue Line rider to pay the same fare from Old Salem all the way to Charles MGH, as another Blue Line rider taking it from Maverick to Aquarium? Salem to Charles MGH is 15x times the distance of Maverick to Aquarium.
Nubian to Tufts Medical Center is only half the distance of Kenmore to Oak Square. Why should a Nubian rider heading to Tufts Medical Center pay the same expensive $1.70 fare as Oak Square to Kenmore? A fare from Nubian to Tufts Medical Center should absolutely be half the fare of Oak to Kenmore. A more reasonable fare system would be to only charge $1.15 for Nubian to Tufts Medical Center, then charge double fares for Oak to Kenmore ($2.30), to cover double the distance.
Of course, since it would be undesirable to have bus riders riding the bus for 1 stop, there'd be a minimum fare of say, the distance of 1 or 2 rapid transit stops (more like 3-6 bus stops, around the distance of State St to either Tufts Medical or Back Bay).
We should be encouraging riders to make more local trips, and allow the MBTA to cover operational costs of running service far from downtown with higher fares the closer to 128 a rider travels to and from (where density and ridership decreases with more distance). Riders riding high ridership routes closer to downtown would pay lower fares, and riders of low ridership routes further from downtown would pay higher fares, with low income fares for those who have no other choice.
For example, if a rider is only paying $0.95 to ride the Silver Line from South End to Downtown, then is considering relocating to Newton Corner. Perhaps a rider would balk and reconsider if the rider realizes his or her transit fare would more than triple from $0.95 to $3.25, relocating from South End to Newton Corner.
If the same $1.70 fare is applying to both South End and Watertown Square, it allows people to relocate further away from downtown and encourages sprawl and super commuting as far as 128.
In addition, there is also cycling to consider. Cycling is likely eating the mode share of public transit, with transit riders switching to biking. Cycling is probably not pulling many drivers away from their cars as much as from transit. By making shorter transit trips cheaper, transit can stay relevant for short trips.