There is a major difference: space. I cannot sit in a ryanair/transavia/whizzair seat for more than takeoff before the person in front has destroyed my knees. Most "premium" airlines have 1-2 inches more space and the option for more spacious seats.
I always buy extra leg-room (like seat by emergency exit), because I am tall as fuck. Problem solved.
I fly a lot with RyanAir, WizzAir and the other discount-airlines, because what they offer is great value - and when you upgrade a bit, it is not terrible.
A ticket listed for 50EUR, I usually end up paying around 100EUR with extras (legroom, luggage allowance).
That is true. Not a major concern for most shorter people though. As a teenager I once did a 12 hour flight (with refuel stop) on a charter 757 with 29" seat space. Didn't find it terribly uncomfortable back then to be honest. Apparently Ryanair has 30" space.