Considering the ATR's are only replacing E170/190's at the moment, I hardly see how they can be losing more money for Virginwest, when they cost less to run than the Ejets over the short sectors they're being operated on.
I think the ATR's are a very smart move for Virgin's economy shuttle runs from Sydney to Canberra and to be honest, with the prices Qantas link charge for their regional tickets, I expect Virginwest to make good inroads into regional transport.
The ATR crews can't be doing too badly with route familiarisation/ airport familiarisation, they're always within 15-20 mins of schedule at the end of the day here in Canberra when they terminate.