sky europe airlines

SkyEurope is not a profitable airline, they're deep in the red figures. I don't know whether that makes them potentionally less save than others. But have you tried the websites of CSA Czech Airlines and Malev Hungarian? CSA is member of Air France/KLM's SkyTeam alliance, Malev is a OneWorld partner. If you add all the knits and bits and fees to the SkyEurope fare the sum might even be more expensive than a city special with CSA or Malev.

I lived in Budapest and used Sky Europe frequently. I only had one problem with a late flight but they accomodated the passengers and I still use them when I travel to E. Europe.