What is the most direct train from Venice to Prague?
You will make a connection in either Munich or Vienna. How to Look Up Train Schedules and Routes Online gives you the DB train schedule link and tips for using it. To compare flights, see www.skyscanner.com.
Its a long trip. There are 2 direct trains every day to Vienna. The first leaves Venice just before 4 pm and gets to Vienna just before midnight, so you would have to get a hotel for the night there before continuing on a direct train to Prague in the morning. The other is a night train that leaves Venice just before 9 pm and gets to Vienna at 7:50 am the next day, then connect to a train to Prague.