It's slightly more than the missed revenue from the failed shakedown. An empty seat is a seat that could have been sold to someone who paid full price. If you hadn't checked in for the flight you weren't intending to take, they could have made a bit more money.
And yet they were so eager to pay the passenger (in the form of a discount) to block that seat on the second leg from being used by a hypothetical other paying customer, even though the passenger being paid to sit in the seat didn't actually want to.
