Train from Prague to Frankfurt

Where did you look? This train planner of the German Railways gives plenty of connections. Some involve a bus (via Nürnberg), others (via Dresden) are train only.

I've been using the DB Rail site via this address: https://www.bahn.de/en/view/index.shtml but it seems I picked the wrong time of day and did not see any trips that didn't involve a bus. I've looked more closely and I see there are non-bus choices. Thanks for pointing that out.

The route using a bus is often the fastest route and the Bahn tends to give you the fastest route, hence you see the bus. There are lots of ways to "trick" the Bahn into giving you the information you want, but you have to know a little bit about the system.

Whereas the direct bus from Prague combined with an ICE to Frankfurt might be the fastest way, there are also four direct ALX train connections from Prague with which you can take an ICE to Frankfurt. The ALX trains take an hour or two longer to get to Munich, but I think I would prefer the comfort of a train to a bus (not that the bus isn't comfortable, but you are freer to walk around on the train). To see the connection that use the ALX train from Prague, select Schwandorf as the intermediate station (the train from Prague stops in Schwandorf, the bus doesn't).

Thanks for the tips but I have decided to stay an extra day in Prague and take an early flight to the Frankfurt airport to catch an afternoon flight home.