I just went on a trip of Austria/Hungary/Czech-land. It really added a lot to visit the small towns of Austria and Czech Republic - Hallstatt, Salzburg, Cesky Krumluv, etc. The problem is that its hard to get to them via train - particularly from central Austria up to Prague. Some of these trains take forever because they are local trains stopping every 10 minutes. In fact, in Hallstatt the train station is on the other side of the lake and you have to wait for a boat ferry to get to Hallstatt. In the case of Cesky Krumlov, we got off the train at 5:00 pm to find a dark and closed train station, a mile from the city center, and no ATM to get Czech money to pay a bus or taxi.
Car rental is not very feasible either since the fee goes up about $350 to drop the car off in the other country. This was the biggest headache of planning the trip.
When we were going to go from Cesky Krumlov to Prague, it looked like a very unpleasant uphill walk for a mile, or summoning a Czech taxi (not so easy when no cars are allowed in the center) to get back to the station, the hope it might be open this time, and then a 3.5 hour train ride to Prague, then a tram ride across Prague and a few block walk. We found a "bus station" on google map, and it turned out to be a large bus stop with no ticket facilities at all. This whole trip from hotel to hotel was going to be about 6 hours.
Luckily we saw an office for a van company in Cesky, and for about $35 each, we had a 2.5 hour trip direct to our hotel - which is probably less than the taxi, train, and tram would have been.
We found that they also run vans to Vienna, Linz, and Hallstatt, and Salzburg. We would definitely do this again. The driver stopped midway, and gave us a bathroom break. He provided some bottles of water to drink. And even carried our luggage up at the hotel.
I am not sure if its permissible to list the name of the company, but you can probably find this one or other ones online.