There's probably just not enough demand to justify the added expense.
Yep, that seems to be it:
MBTA May Terminate Night Owl Bus Service - The Tech
Unfortunately the Commonwealth doesn't give the MBTA actual money when they prevent an accident, so the current system will stay in place until the someone with authority decides its a priority.
I agree, all night service, even extremely sparse, would be nice. I really don't like it, though, when people use the T being closed as an "excuse" to drive around drunk.