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Ryanair - News : Ryanair To Go 100% Web Check-In From October
From March states that the web check in will apply to ALL new bookings except promo fares, which would of course suggest everyone will have to pay it, including hand baggage only.
The majority of pax who use checkin desks or check in bags are used to getting robbed of their hard earned. I would imagine that it will be quite a shock to some of the army of hand baggage only pax. This is one arguement that you wont see at the airport though (unless the boarding pass needs reprinted) as it will have to be paid at the time of booking.