Český Krumlov is magical even in the rain. You can take a tour of the castle, go through the interiors and the castle museum. A visit to the graphite mine is a great experience - you will get a helmet and a raincoat and take a ride on a mine train underground. Children and adults usually enjoy it very much.
Those who like history and a bit of mystery will appreciate the wax museum or the torture museum - not suitable for very young children, but very engaging for older ones. There are also a number of cafes and galleries in Krumlov where you can take shelter from the rain. And don't forget to visit the castle's underground, which has its own unique atmosphere.