There's an OBB routeing via Linz which looks better than the 5-hour bus ride from Munich:
Zurich 0840 - Linz 1506 (Railjet 163)
Linz 1535 - Prague Hlavni 2039 (Rex 1542)
This is for a random date in July (98).
I've done Munich-Prague via Vienna - very easy.
From Zurich you can just do it in a day but nicer to overnight in Vienna.
There are 39/29 fares on each leg.
http://www.oebb.at/en/
You normally have to change stations in Vienna (Westbf to Meidling).