Typically, elites with appearance fees will have a "cut clause" in their contracts, whereby they'll have their fee cut by certain percentages if they don't achieve certain levels or performance.
For example, a 2:08 guy would have a clause that if he doesn't break 2:12, his fee is cut 50%. Sometime's they'll give a break for that if they still finish in the top 5, or they'll have different allowances for inclement weather.
Most of the time, a finish slower than the cut time is treated the same as a DNF. Since so many people at Boston weren't going to hit their time (maybe even a more generous inclement weather time), they bailed. But they still got paid.