I had a strange experience recently trying to book a ticket through Hipmunk/Orbitz. I found a ticket. Tried to buy 3 times. Each time it said the ticket was no longer available, but it kept showing up in search results (stale cache on the server?). Same ticket was found on the airline's website for $20 more, which I was able to purchase.
Why it's more expensive to purchase direct, I don't understand.
Airlines and hotels often have agreements with the aggregators that they will not offer fares lower than what they are making available through the GDS aggregators.
This is why hotel sites will offer discounted prices based either on prepayment, or package deals, so that the price isn't directly comparable to Expedia, etc. It's also why those deals are sometimes the best - with sites like Expedia/Travelocity taking something like 30-40% of the nightly rate (versus a much lower % for airline tickets), hotels should be willing to bend over backwards to get you to book directly.
Also, it's possible to put a hold on a ticket without buying it; I'm guessing here, but if you're looking at one system the available fares list might reflect that some seats are on hold (by not showing those fares), while another system might not, resulting in different fares being visible... that will generally show up as a difference in the lowest-priced fare, since most of the search sites highlight that parameter when displaying search results.
I'm also scratching my head as to why we're now ~3 (maybe 4 counting ITA?) levels deep for purchasing of airline tickets? Hipmunk -> Orbitz -> ITA -> Airline
There is a lot of "slack" in how travel is priced due to all kinds of agreements about what rates you're allowed to show. That's partly why package deals can be so good. These are not simple problems to solve, even in a best-case scenario.
Sometimes you can actually game this. For example, I have noticed cheaptickets.com sometimes fails to update their prices quickly enough. All of the other websites have moved their prices to the new fare, but they slack behind. I know there is an issue since the airline does not ticket their mistake immediately (i.e. make the ticket more than a stub and actually consummate the transaction). I wonder who takes the hit on this?
If you look into all of the issues surrounding the United and Continental merger, there some fascinating material exists on airline reservation systems and back-ends. In summary, I think they get build to defense contractor standards, which does little to reassure me.
Why it's more expensive to purchase direct, I don't understand.