Because my travel is generally for work, and when it's for fun AA still manages to serve me well, I'm not a frequent user of any of the low-fare websites. I want to know what airline and what flights I'm buying and I want the ability to earn miles and get upgrades.
On the example I gave in my earlier post, I used AmexTravel (formerly ITN), and Travelocity to get fare quotes IAH-MIA. I know I didn't see any fares offered for AirTran, so I can't say what they might offer. The fares that did come up in my search, with CO, AA, and UA, were all over $400. That wasn't Labor Day weekend, either, but the following weekend.
So I can't say whether Hotwire will be a good site or not, but it did seem to offer a good alternative to what I found on the sites I looked at. I imagine, like all the other lowfare sites, it will take a while to get significant inventory in the system.