I gave a decent (well, at least a lengthy) answer to this question here:
http://news.ycombinator.com/item?id=1473748Basically, getting the raw data is quite difficult, but once you have it, you need to expend a really enormous quantity of engineering work into using that data to get useful answers.
For example, ITA invented a language to describe taxes. That's because the tax code changes all the time and is incredibly complex. There are fares which different entities in the airline industry price differently due to tax code ambiguities. The search problem is really very hard once you have the data.
Now, ITA software does offer their flight search engine as a service: you sign a contract with them and issue queries and they send you responses. I don't know how interested they are in cutting deals with really tiny startups, but they might be amenable. You will of course have to pay in some fashion: maybe a fixed fee per query or pay per compute time or pay per successful booking.