(1) They don't own any relationships with suppliers. UI/UX matter, but any business owner will tell you that those relationships are where the money is. Hipmunk still has to give 50%+ of it's earnings away to those who own the relationships.
(2) Hipmunk's differentiating factor is its UI/UX, but frankly, I don't think it's all that amazing. Its structure and optimization are great for nerds like me who read hacker news, but try getting your parents (or people who spend big bucks booking travel) to use it. I have, and the resounding response is how difficult it is to use. Again, there is a market for their product, but I think it's designed by nerds for nerds
(3) 1 million flight + hotel searches a month is actually nothing with respect to the market, especially considering how much I see ads for hipmunk. Anyone can make a white-label travel site and pay for traffic.
I'm not trying to be a contrarian just to be an asshole. And Hipmunk might have great things in the pipeline, but for now, they're one of hundreds of travel sites in my opinion.