I think I would rethink the decision to drive. Remember, the train is city center to city center.....driving is "somewhere near the city". You also have to get rid of the car, pick up the car (and make sure it complies with all the rules for driving in other countries), and I can almost guarantee the train is considerably less expensive. Germany has the Autobahn, the Czech Republic does not. I'm sure I'm missing some items, but arriving in town rested and relaxed is far more important.
Rail is not the preferred choice on this route
Take the nice modern bus via DB Bahn around 5 hrs and affordable..or even consider FLIX Bus service
There is no real need for a private transfer unless you just wanna spend the money.
Just take the train, a leisurely ride through the countryside in 5h42 with a good book and bottle of wine or some beer!
I'd fly. It's a quick, cheap flight. 1st class on a train would be my second choice. I couldn't ride a bus for 5 hours.
The German bus is the best choice on this route.
Bus takes 4.5 hours centre to centre, which is approximately the same as it would take you flying, centre to centre, but considerably cheaper.
Consider whether you would prefer to be cooped up in a car for that amount of time vs. in a spacious double-decker bus with wi-fi, etc. Take a good book and a picnic and you'll be there in no time. €29 from www.bahn.com
The train is slow and old-fashioned, but use it by all means, if you don't mind that sort of thing.
First class is identical to second but costs a lot more
I read that it takes 4 hours by car and it takes about 6 hours by train. I also have seen private transfer prices almost at the same cost or less than 3 adult tickets for the train. Three adult tickets on train will run me about 400 EURO or about $477 USD. The transfers with www.ckshuttle.cz/bus-cesky-krumlov-transfer/ will cost 8.400 CZH about $340 USD plus tip.
Flying times non-stop were not times I wanted. Also gets costly with paying extra for luggage and 3 passengers.
Has anyone used CKShuttle??
If you were to go by car (door to door service) I would suggest you use a company based out of Prague - some charge the same price - and you can be assured the driver will be fresh as opposed to using a company based over two hours away from Prague.Edited: 17 January 2016, 11:40
I don't know where you've been looking for prices, but if it is Rail Europe then don't - it is a massive rip-off reseller.
The train costs from €19 each (but you can do it for maybe cheaper than that if there are three of you and you use a Bayern-Boehmen Ticket), and the bus from €29 each, which will take about the same time as a car.
Last time I took this route during the off season via the DB Bahn bus....there was a whopping 7 people on board-both directions .....I'd hardly say cramped