I don't think the fares are that expensive.
That is you view and respect people will have different view as mine, but I still say the single and Daily fares outside Melbourne zone 2 are too expensive and how they're workout is unfair compare to Melbourne fares.
The Nar Nar Goon person you mentioned above has a number of benefits not available to suburban passengers (express train, faster travel times, etc.).
Yes they also get a choice of fewer services. But in peak times (and you've quoted the peak fare above, not the off-peak fare), you have advantages from avoiding traffic congestions. I don't see the current fares as being too cheap (and of course they were reduced in price some years ago). Other thing to factor in is that Victoria has one of the most generous concession schemes in Australia - which means that people on low incomes (eg. a low income health care card) pay 50% less than adults - unlike some other states where they have to pay full fare)
In off-peak time miss a train from Nar Nar Goon and then can be wait up to 3hours for the next train service.
A person should not be forced to pay nearly double for their fare because they are travelling 7km more.
In my view the Traralgon line should be electrify and with new train sets like the CityRail H set that has Capacity of 864 seats compare to V/Line which currently has Capacity between 178 to 285 seats.