Since the merger of the SPL and SFL, the prize money has grown significantly. For example, when we won the league in 12/13, we received £60,000 as prize money. Forfar Athletic, who finished midtable in League Two, received a payment roughly equivalent to that this season. The Championship ranges from 500k to 250k depending on finishing position I believe.
Taking the money from playoffs to fund parachutes keeps the overall payment in place and only affects teams who are playing, in effect, bonus games over the 18 issued at the start of the season - better that than taking it out the full pot.