While their base ticket prices may seem incredibly low, they make their profits by tagging on extra "service fees" that appear on their website after you've begun checking out. For example, a few years ago I remember I had to pay extra for "baggage insurance", which ensures that your bags do eventually make it to their intended destination and don't get lost, something that is usually implicitly included in the original ticket price of other airlines. The UI of the Ryanair website stresses the importance of this baggage insurance with a popup window. Other airline comparison sites probably have decent UIs that don't push these options to the extent of Ryanair.
They also go to great lengths to cut any cost. I've heard that employees are not allowed to charge phones at work in order to save on energy bills. And from my experiences, their employees really don't seem to have any sort of customer service training. Or maybe they're just grumpy because Ryanair treats them so poorly.
http://en.wikipedia.org/wiki/Ryanair The Criticisms and Complaints section is actually pretty interesting.