Do you have a train specific discounted (Europa-Spezial) ticket, with the express bus from Prague, or do you have a full fare ticket or a rail pass with a reservation? If you have a train specific ticket, there is a clause in the AGB that says that if you miss the connection because of the Bahn's fault, you can take the next available train. I tested that provision (not on purpose) in 2008 when my local train from a small town at the edge of the Harz was late and I missed my connecting IC (part of a Sparpreis ticket). I went up to the ticket counter, he confirmed on his computer that my train had indeed been late, and changed my ticket. The following express train was an ICE.
I would assume they would do the same thing for a reservation with a pass or full fare ticket, but a full fare ticket is usable on any train. The most you would have to buy (and I think the Bahn would take responsibility and give you a new one gratis) would be a new reservation. If your bus is late, mention your connecting train to the driver (I think there is actually a stewardess on board). If you are just taking a regional or local bus to the station, the Bahn probably won't take responsibility.