The role of the Federal Government is to not necessarily maximize financial return. The argument that jetBlue greatly benefits actually might work in Spirit's favor. Spirit's best argument is the downward pressure on airfare they create when they enter a market. jetBlue losing a key competitor won't drive down prices. Helping the little guy has rarely been bad politics.
Don't forget, U.S. commercial aviation is the least free market, most regulated industry in this country. Government involvement isn't uncommon.