I'm willing to bet that it's because there's no passenger friendly way to get down to or up from the ramp, or for a bus to actually pull up. Since the advent of the jetbridge Logan never really had ground stands, beyond that for prop regionals like metroliners and 1900s, but I would be willing to bet passenger ramp access was never provisioned into terminals A or E. It'd be an investment to reconfigure the holdrooms, punch through the wall and basically shim in a new gate with a ramp or other structure to get passengers down to the ramp. The terminal shuttle buses I'm most familiar with is Uniteds at Newark and those at LAX where they basically built out a full gate for the thing with exterior stairs bus berths, shelters and elevators, or a rather long switchback ramp. I don't think there's room for that at Logan. As such, you'd basically have to give up a gate in both terminals, and kinda do what Cape Air is doing.
I'm told that the Cape Air / Boutique boarding experience is a particularly unglamorous affair involving a slightly perilous climb down the stairs on the side of a jetbridge. Mind you, I've never done it myself, but I suspect it's a lot easier to sell that for 9 people climbing into a Cessna to Martha's Vineyard, or for someone getting the Delta porsche transfer experience, rather than people expecting to get to their international widebody business class seat - especially since they'd have to climb up again.
*Edit: I also realized this just now: unlike a lot of other airports like Newark, Logan doesn't have a separated airside service road, outside from a short stretch at Terminal E. The Logan roads are such that they run around the outer edge of the terminal footprints, such that any shuttle would basically would constantly be stuck waiting for aircraft.
