Is there a train that leaves from Ceske Krumlov to Vienna?
Looks like you pretty much have to change at Ceske Budejovice and Gmünd.
This is a private shuttle bus service;
http://www.shuttlelobo.cz/shuttle/index.php?artid=2&lang=en&mode=normal
It looks like about $60
The train is a problem because first you have to backtrack to Chesky B. on a VERY slow train (and the Krumlov train station is quite a hike from the old town), then switch trains to a slow Czech train to Linz, Austria, then change trains again. It takes a long time. The shuttle bus will get you from place to place in comfort, faster than the train (that's why the shuttle service exists).
You can also take the shuttle on a shorter trip to Linz ($25) where you can get a fast train to other destinations, or take the train from there to Vienna (90 minutes, maybe save a few $).
Thank you all for the info. We have decided it would be much easier to take the shuttle. We will save our $ for beer when we get to Germany.