air berlin has only connecting flights via nuremberg which may be more expensive.
ryanair has nonstop flights from "Frankfurt-Hahn" to "Bratislava-Vienna" as of October, 31st with low fares but remote airports. expect longer busrides from Frankfurt downtown to Frankfurt-Hahn (2 hours) and from Bratislava to Vienna downtown (1 hour).
Be aware that Bratislava is in Slovakia where "schengen visas" are not valid.