It depends. Are we going down the well travelled path of just looking at the financial returns of a route. Some (by no means all) don't pay for themselves in purely financial terms, however, they tend to offer benefits to the local community which aren't received in the fare box.
Theoretically, this sort of traffic could be catered for by long distance bus transport, however, in reality buses don't provide the speed, comfort and, crucially the same ability to keep connections with the rest of the network.
This is apart from the benefits of secondary routes as a feeder/distributor network for the Inter-City lines.
Seems to me the Greeks need to be getting more bums on seats. If they have to drop prices it may not lead to a financial improvement straight away, but the cost per passenger kilometer will get better and the indirect value of the railway to the wider economy will increase.