I think people forget just how many flights these aircraft operate. It is very easy to pick up delays on the ground - I flew with Flybe only the other week and we were on time boarding and pushing back but held up 15 minutes during taxi and holding for departure. If that happens a few times in a day that's an hour delay for those on the aircrafts last sector of the day.
Easyjet and Ryanair aircraft spend more time in the air and therefore pick up marginal delays which seem unnoticeable. Flybe is in and out of airports all the time - this also means minor mechanical faults develop.
It's like driving your car every day for hundreds of miles compared to someone who drives theirs for a few miles. The most used vehicle will need servicing or repairs much more frequently