I'm not sure if you're confused about what Skyscanner does? Skyscanner, like flights.google.com, Kayak, etc. is free to the user - they make their money on referral fees, among other things.

And, for that matter, flights.google.com is based on their acquisition of ITA Software for $700M in 2010, so clearly there is a market for companies like this: http://www.google.com/press/ita/