I suspect it comes of thinking of the Commuter Rail lines as necessarily low-frequency (or mostly-rush-hour), low-passenger-count services like the ones the T inherited, instead of potential high-frequency, high-passenger, all-day services. (I know there are midday trains, but many fewer and not really emphasized.)
Not having the money to pay for electrification probably also plays a part.
And the politics of CR probably feed that, too. Out in the suburbs, a lot of people who don't use CR clearly wish it would go away; a few people near terminals might welcome electrification because it would eliminate diesel idling, but more people would probably oppose electrification because the wire are ugly (they are), because electrification probably means more trains and therefore more instances of noise even though each train is a little quieter, because more trains esp in a regional rail pattern means closer ties to the city and "more of those people from the city coming out here" and because they are afraid of the electricity in the wires (I remember this in Rozzie and Hyde Park in the 1990s when Amtrak electrified). Meanwhile, in the city (Boston, Quincy, Brookline, Cambridge, Somerville, Chelsea, Revere, Medford, Everett, maybe a couple other cities and towns in the generally urban rather than suburban zone) a lot of people would see commuter rail electrification as a waste of money that should go to transit instead, and a way to make the CR tracks through their communities uglier and more dangerous (see comment about Rozzie in the 1990s). So I suspect the T's leaders just don't see a political or passenger-count possibility of electrifying.
It kind of goes along with how, at least as far as I know, the T doesn't really advertise all the cool weekend destinations you can get to by CR, except maybe via the ski train to near Mt. Wachusett. What would it cost to put up posters in the subway stations advertising x trains per day to Lowell in walking distance of its National Park; x trains a day to Rockport, where you can walk to a fun little beach and a bunch of shops and restaurants and get shuttle buses to other places in town; x trains a day to Providence (well, maybe Mass would disapprove of that one); Newburyport?
Concord incl Walden Pond not so far from the station? Scituate? Even Needham Ctr is a cute little town center with nice places for lunch that feels very different from the city and makes an easy CR excursion when the weekend trains are running.