There's sometimes competition for the best stands with certain airlines getting priority. It can be a hassle for the airline with the tight turnaround that low-cost airlines often have. They've to get people off, clean the plane, do the statutory checks of each seat and get people boarded in remarkably little time.
This right here is why I don't want to work for Ryanair. Trying to clean down a plane in tight conditions in the space of 20 minutes seems almost impossible to me. That's a LOT of seats to get through.
I don't see why there is such animosity towards budget airlines. No-one complains about budget bus companies, you get what you pay for. I personally think that, for so long, flying had an air of grace to it. People complain about flying economy class on long haul flights, but it's never great being stuck in a tube for 12 hours. I think people assume that they should have Long Haul level comfort (keep in mind the RyanAir "bus" style seating with no booking and no reclining is a relatively new concept) on the short haul budget lines. Just sit down, be quiet and get on and off in an orderly fashion. It's not so much to ask.