The line from Bellows Falls to Rutland is still running... with the painting of most locomotives to red (and now "Vermont Rail System"), they are trying to make it look like one big system. Essentially it always has been, but with the separate subsidiaries (VTR, GMRC, CLP, NYOG). It appears the passenger trains aren't even being marketed as "Green Mountain Railroad" anymore, but instead, as "Vermont Rail System - Passenger Services". The only thing they appear to be running still is the dinner train, out of Burlington, and that is done with the "silver fleet". The "green fleet" has been retired or I believe sold.
Its too bad, considering at one time, GMRC ran passenger excursions out of Burlington, Bellows Falls, Manchester, and White River Jct, sometimes 3 locations at the same time. I'm glad I rode those trips when I did, riding I believe what was the last true "Rutland Limited" from Bellows to Rutland, plus several excursions on the "Conn River Division" covering WRJ to Lyndonville in two separate trips... both to Farmway I believe.
Freight service must be paying the bills pretty good, without the need to have passenger op's interfere.