Probably not. I am unsure what you mean by paying “with transit value” but Massachusetts says a "Stored-Value" Charlie Ticket does not qualify for the commuter deduction.
MBTA Passes eligible for the Commuter Deduction. Any MBTA commuter pass or Charlie Ticket that is designated to be a monthly or weekly pass is eligible for the commuter deduction. The MBTA commuter rail "Twelve-Ride" pass and the MBTA express bus or commuter boat "Ten-Ride" passes qualify as weekly passes eligible for the commuter deduction. However, a "Stored-Value" Charlie Ticket does not qualify for the commuter deduction.[2]
[2] Stored-value Charlie Tickets are sold by the MBTA to replace payment by tokens or cash.
A stored-value Charlie Ticket will have the fare deducted from it each time a patron rides the subway or bus.
TIR 06-14: Personal Income Tax Commuter Deduction