You can check for the best bus and train connections HERE . There you can find the public transport connections for Prague and České Budějovice as well.
From the airport in Prague, take the bus "airport express" that goes directly to railway station (last stop). The bus leaves from the airport every 30 minutes. Bus station is between Terminal 1 and Terminal 2. You will buy the ticket at the driver for 60 CZK.
You can also fly to Vienna airport. From Vienna you can take the train and/or bus to České Budějovice (or use the shuttle (https://www.ckshuttle.cz/transports/transfer-from-vienna-to-ceske-budejovice/).
1/ Trolleybus: line 3 - bus stop “Jihočeská univerzita” going from railway/bus station (bus stop is called “Nádraží” through city centre; you can buy a ticket at the ticket machine (16 CZK – you need coins or a wireless bank card for that) or by a driver (25 CZK, cash only). There is a big shopping centre (Mercury) just next to the train/bus station near the “Nádraží” bus stop.
2/ Taxi: the cars are standing in front of the train station. The price should not be higher than ca 200 CZK.
3/ By foot: It takes about 15-20 minutes by foot from the city centre, 40-45 minutes from the train/bus station.
For navigation we recommend to use: http://mapy.cz/ where you can find location of bus stops together with link to the schedule as well.