we would love to rent a car and take the ferry from Ancona to split but the drop-off charges are astronomical. Our final destination is Budapest where we take a river cruise to Germany. Does anyone have suggestions on how to manage the ground transportation so we can do some touring on the way?
You might look at a train from Venice to Munich, see Munich for a day or two, then go on to Budapest on the night train out of Munich. Me? I would spend a lot of time sight seeing around Venice by car, then hop a flight to Budapest and use more time sight seeing in Hungary.
I would fly.
If you pick up a car in Venice, then there should be no significant fee to drop it at another city in Italy, such as Ancona (for the ferry) or any Italian airport. If you want a car on the Croatian side, rent it separately, but there would be a drop fee to leave it in Hungary.
Direct trains from Zagreb to Budapest run twice per day, take 6.5 hours, and tickets cost perhaps $50 per person, 2nd class, to buy in Croatia.