Simon,
I don't think anyone is suggesting that liveaboard operators ever enjoyed direct government fuel subsidies. Rather, everyone buying fuel (including you and me for our autos or motorbikes) have indeed been the beneficiaries of the Indonesian fuel subsidies, which have applied to all automotive petrol/gasoline, diesel, as well as "elpiji" (LPG gas) and kerosene used for cooking sold in the country). The list of beneficiaries has included liveaboard operators (and passengers) as well.
The 30% across-the-board increase in retail fuel prices in May, the first since the last big jump in 2005, was actually just a cut in the level of subsidy from completely unsustainable levels to the merely insane. Indonesia will still spend somewhere between US$20-30 billion on fuel subsidies this year, almost a third of the national budget, more than any other country in the world except China. However, fuel is still subsidised. The new official price for diesel, Rp 5,500 / liter (about US$0.60) is still well below world market prices. How much Jakarta's fuel final total fuel subsidy bill will finally end up at depends on where the price of crude goes over the next five months - the price was around US$117 a barrel when Jakarta cut the fuel subsidy in May.
Boats bunkering (taking on fuel) in the outlying islands have often had to pay higher prices than the official numbers. Distribution and sale of fuels down to the depot level is controlled by the state-owned monopoly corporation Pertamina, but the Pertamina system of distribution throughout the archipelago is "a failure", as an article in today's Jakarta Post put it. Local distributors in outlying places like Sorong are allowed to add on their own surcharges on top of the Pertamina base price ostensibly to cover the costs of transporting fuel from Pertamina's central depots. People have been complaining about this for years, but it hardly matters. In the worst case, the price of diesel and kerosene sold on the farthest outlying islands can be double the price in Java or here on Bali.
In reality, moreover, what seems to be happening now is that fuel distributors are simply holding fuel off the market or imposing much bigger "local surcharges" because almost everyone believes that the government will be forced to reduce subsidies by raising fuel prices again, possibly soon. This practice is prevalent in the outlying parts of the archipelago, but it isn't unknown even here in Bali. You may have noticed, Simon, as did I and many other drivers, that many Pertamina petrol stations suddenly and mysteriously "closed" or "ran out of fuel" the week before the subsidy cut and price hike last May.
This seems to be happening again. When I was in Komodo in July, two liveaboards (no names!) were about to be forced to shut down operations and shift their guests (who had already arrived in Bali or Labuanbajo) to other operators because they were unable to purchase fuel in Flores at any price. Other boats with better connections to dealers were getting fuel, but my understanding was that everyone who did get fuel was being forced to pay a hefty surcharge on top of the new prices.
Nothing I've written her should imply that tolerance of operators who use rumors of fuel price increases as a pretext to impose an unnecessary surcharge on guests. I also agree with Simon (and Drew) that costs need to be shared fairly among the all the guests, including those who booked early and late. Personally, however, I also believe people who booked and paid for their trips in advance with the understanding that they had paid in full should be given the choice of paying the surcharge or else backing out, with a full refund of all monies paid. I can also see that this may not always be possible. This is a difficult situation, things probably need to be approached case-by-case. It's very important to be dealing with people you trust.
Robert Delfs