Monkey Mia has a very small population, possibly lucky to be 200 people. It is a tourist destination due to the dolphins.
Carnarvon for many years had a sign stating the population was 6,700 (its post code is 6701) but I see in the 2016 census it has reduced to 4,426.
Flights seem a bit cheaper these days but Peth to either Monkey Mia or Carnarvon will still be around $500 return (some days more some less). The flight between Monkey Mia and Carnarvon is a bit over $100.
There is not a large fixed population to support large aircraft on these routes. Due to the vast distance between towns in WA particularly north of Geraldton and the high costs of all flights very few tourists use air travel as a mode of transport. Most tourist that come to this region use campervan or caravans as there are many places to see along the way that have no air services.
Many residents of Carnarvon simply drive to Geraldton to buy any goods they can not find in Carnarvon often things like white goods and then they drive them back and use them that day not 2 weeks later. After Carnarvon living Perth is too busy and big for many and only visited to fly out some place else like Bali for a vacation.
I think you would find Carnarvon - Darwin, would be get similar if not better traffic than Perth. The reason is Carnarvon has a high migrant population and heading towards Singapore rather than away from it is appealing.