Ryanair (and several other low-cost carriers) require that non-EU/EEA citizens present their passport for a visa check at the luggage counter:
Irrespective of a passenger's visa requirements, all non EU/EEA citizens must have their travel documents checked and stamped at the Ryanair Visa/Document Check Desk before going through airport security.
However this seems to conflict with EU's Air Passenger Rights regulation, which only lists the following reasons for denying boarding:
Paragraph 1 shall apply on the condition that passengers:
(a) have a confirmed reservation on the flight concerned and, except in the case of cancellation referred to in Article 5, present themselves for check-in,
— as stipulated and at the time indicated in advance and in writing (including by electronic means) by the air carrier, the tour operator or an authorised travel agent,
So as long as I present myself to the gate (with a passport and valid visa) at the specified time, the airline is obligated to either allow me to board or cancel my booking and issue compensation as per the EU passenger rights?
As @Moo mentioned in his answer, I may also be denied boarding for:
reasons of health, safety or security, or inadequate travel documentation
But if I have a passport and a valid visa, is my travel documentation "inadequate"?