I've been checking in online for Ryanair flights for quite a while without paying to do so. In fact, checking in online, as far as I remember, saves charges.
Please show, from the Ryanair website, where it says there is a charge - you know you can't believe all reported data by 3rd parties.

Sorry, I found the Ryanair info in their 'news' page. That's outrageous, and I suspect it will be challenged legally.