Ryanair's fares, even with the 'add ons', still generally work out far cheaper than those of most other airlines. So you're still getting a bargain.
As Ryanair always point out, most of the additional fees are avoidable. For example only 40% of their passengers take hold luggage or otherwise need to check in. The majority of passengers just take hand luggage and check in (for free) online. (On many of their Stansted-Dublin flights, not a single passenger will use the check-in facilities).
The card handling fee is a bit annoying but regular flyers simply apply for a Visa Electron card, which doesn't incur any booking charges.
Chris