Given that skyscanner doesn't find easyjet results for me, nor does it find ryanair I'm going to guess that they don't let these services pull in their data to consumers. I am guessing this is an ownership issue, and that they want to process customers themselves, rather than through resellers.
Note that sometimes you have to click the "show all" link at the top of the search results to get low-cost airline results to appear. (This is possibly revenue-related.)
Skyscanner shows budget airlines (including both Ryanair and easyJet) along with 'traditional' airlines (BA, KLM, Virgin etc etc). In fact we show almost every airline in the world.
If you are searching for a route which you know Ryanair/easyJet to fly but we are not showing it, please do contact our customer feedback team (http://www.skyscanner.net/contactus.aspx) with the details and we'll investigate immediately.
Most low cost carriers aren't willing to pay to be listed in Global Distribution Systems. Kayak is linked to Amadeus and Matrix to ITA, so unless extra development is done, they will only list flights from GDS-listed companies
