They did the math more extensively than your back of the napkin math. Unlikely that they suddenly realized that none of their prices all along made sense. They've been organizing flights for years. More likely that their price was based on an agreement with an unestablished company, that screwed them over at the last minute and didn't show up with the promised goods.
If you want to put your head in the sand that's YOUR choice, but if you want to make the math, you will see what these things cost ALOT OF MONEY (look above thread somebody with charter experience says that they HAD to charge $600 per person for a simple TLV-WAW flight which is MUCH shorter) especially when the plane flies back EMPTY or sits dormant for a week or 10 days for the passenger to come back home.
It never made sense, and it will never make sense, and whoever thought that this will work was a fool to begin with. They either googled "private charter flight" and some Nigerian scammed them with a low price, or better yet they were miscalculating things, they thought that will be able to sell premium seats for MUCH more than they actually could sell it for and they were in a hole for a couple hundred thousand dollars.......And of course the airline said no money, no honey, there is NO plane flying tonight unless we get our money. So they decided that this has to be recalled.
I really pity these guys and I am not sure that if I would be in that industry if I wouldn't try that same gamble, but at the end it was a gamble, and unfortunately for boths sides it didn't work out.