Kayak makes around half their revenue from referrals and the other half from advertising. There's no reason Hipmunk couldn't settle for less revenue per search.
They have fixed costs (independent from the number of tickets bought) in the form of payments for search results to ITA plus whatever company overhead (maintenance, salaries, etc).
Whether Hipmunk can afford improvements in user experience while earning thinner margins than the competition is not entirely obvious to me.
I do hope they make it though. Hipmunk rocks!