So not only are they out $50 on you, they're potentially out an additional $150 on the unsold seat.
Only if you don't count the $250 they already got for the ticket you bought. Their complaint (on that issue) is that you're buying a cheaper ticket than they wanted to sell you. Everything else is smoke and mirrors, which amount to "we want to sell the same seat twice, and we can't when you do this, and we don't like it even though we couldn't if you bought the ticket we wanted to sell you."
The one real issue I see (as mentioned in TFA) is that when you skip the second leg, they will wait at the gate until they're sure you're not coming. That can, and I expect, does, make flights leave later. Not necessarily late, per se, but later than they might have otherwise. They can't really delay the flights very long over this, so in the long run, it means that they'll end up making less effort to wait until people who are running a little late (because their first leg was late landing) are at the gate.
In short, the airlines lose nothing, and overall, probably make a little bit more, and other passengers are inconvenienced, but probably not much. So this must be a day that ends in "y."