Originally Posted by
potfish
You were looking at the wrong thing. Non-EU spouses do have the right of free movement. What they don't have is an automatic right of settlement in the country of which their spouse is a citizen... because national law takes precedence over EU law when it comes to a country's own citizens. So, for example, a Russian married to a UK citizen has the right to accompany their spouse everywhere else in the EU, but does not have an automatic right of settlement in the UK.
Forgetting the families angle, legal residence in the UK is not enough to get you into other EU countries without needing a visa (first hand experience of helping a UK-resident Zimbabwean friend get a visa for France) so it's expected that Ryanair should check non-EU passport holders have the required documentation for their destination.
But they could do this at the gate - that's what other airlines do. There is no need to require someone to go to a check-in desk just to have their passport examined.
The argument is then whether it's fair for them to charge only the affected passengers for this extra procedure, or spread the cost amongst everyone.
Airlines are required to examine ALL passengers' travel documents - it's just the thoroughness that varies. EU passports tend to get a cursory glance. US and Canadian passports tend to get a slightly less cursory glance. The only passports that need to be examined more closely - and only for flights that are not intra-Schengen - are those of nationals who need visas. And even that only tends to take a maximum of half a minute.
There simply is no justification for making non-EU nationals check in at the desk. But, as the previous poster said, a successful legal challenge would probably mean that everybody would have to pay a "foreign passport fee" in the same way that everybody is now paying a wheelchair fee when flying Ryanair.