I don't really understand the question. They run a comparison service just like many others do, but probably they are one of a small handful to reach critical mass and thus be widely used, along with Kayak.
You ask why not hundreds of sites but really, can you off the top of your head name hundreds of sites that provide the same service for anything? Basically there isn't enough differentiation feasible in this sector (find the cheapest price for a given set of parameters), so you'll just have a handful of popular sites, even if you had 100 sites all basically the same, some would naturally get more popular for whatever reason, typically due to being one of the first to offer a service of sufficiently good standard, and snowball due to word of mouth / passive advertising etc. Skyscanner was launched in the early noughties so probably had first[early] mover advantage, bearing in mind aggregators / comparison sites were in their infancy back then.
So let's say you have a rival site you are going to launch, basically it is almost impossible to offer a better product in the rawest sense, because the product is information harvested from elsewhere, but from a limited set of providers (it's not like there are a huge range of popular airlines not listed on these sites already). The only way you could catch up with a giant would be to offer a better service.... perhaps better filtering, alerting, etc etc and then invest sufficient in marketing to get people to try your product and determine that it is superior.