I would never even consider flying the BUD-VIE leg - with all the hassle of getting to/from the airports, checkin times, security, etc + packed into a small plane VS downtown-to-downtown, walk around, have a nice lunch/dinner (on the money you saved on the tix). Door-to-door about the same time, too.

VIE-PRG I cannot comment on, it's been over 10 yrs the last time I took that train, then it was 4 hrs, I guess shorter these days.

Flying PRG-BUD can be a good choice.