Earlier quoted context omitted.
I could be mistaken, but from what I'm understanding is that Booking.com books the flights for you, by automating the booking process on Ryanair (and subsequently add their own fees), whereas the likes of SkyScanner show you the information, then direct you to the Ryanair website to book through the airline.
Which is actually convenient for booking users. The Ryanair website is a big mess.
Meanwhile booking.com has a recurring pattern of diverting you via search results to show you extra sponsored results. My experience is that Ryanair is far easier to navigate and book than Booking.com