There are several ways how to travel from Munich to Cesky Krumlov.
Prices of all three options are very similar and the biggest difference is the time it takes.
To get from Munich to Cesky Krumlov by train, you need to take at least 3 trains:
In average it takes 8 hours (plus the time needed for transportation from your hotel to train station and the other way around)
A little bit faster option is replacing the last slow train connection by a bus connection:
This journey takes 7 hours 28 minutes in average (plus the time needed for transportation from your hotel to train station and the other way around)
The easiest and most comfortable way. Shuttle service picks you up in your hotel in Munich and takes you directly to your hotel in Cesky Krumlov. You will not have problems with searching the bus (train) station and you will not need to worry whether you catch the right bus (or train).
The ride with shuttlebus only takes 3.5 to 4 hours.