I do have a few problems with it:
1. There have been a few times that I have found a flight only to click through to another online flight aggregator (orbitz etc) to find they don't have the rates specified on hipmunk. Very frustrating.
2. I hate, hate, hate dealing with other aggregators (again..orbitz etc). I don't know if they do this already or it is in their long-term plan, but Hipmunk would benefit from working directly with Airline companies. Apologies if they already do this and I didn't see it.
3. This is less of a problem and more of a request: rental cars! Please do for rental car search what you did for flight search. It took me hours to find a car to rent after searching through the usual suspect's websites (hertz, budget, avis). Their websites are beyond terrible. For example, I went to select the pickup location for a rental car (on Budget) and when I clicked the location, the page reloaded with zero error feedback. I assume there was a problem with my selection but how was I suppose to know what it is? I clicked all the options and it just kept reloading the page. Terrible.
Hipmunk is a great product tackling a hard problem. However, they have a lot of work to do. I will continue to use them and hopefully they will continue to improve. Great job so far.