There are several ways how to travel from Cesky Krumlov to Munich.
Prices of all three options are very similar and the biggest difference is the time it takes.
To get from Cesky Krumlov to Munich by train, you need to take at least 3 trains:
The average time is 8 hours (plus the time necessary to get from your hotel to train station and vice versa)
A little bit faster option is replacing the first slow train connection by a bus connection:
This journey takes 7 hours 35 minutes in average (plus the time necessary to get from your hotel to train station and vice versa)
The easiest and most comfortable way. Shuttle service picks you up in your hotel in Cesky Krumlov and takes you directly to your hotel in Munich. 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.