We need to ravel form Montenegro or Dubrovnik to Venice in mid-June. Thus far, it looks like our best bet may be driving to the Istria peninsula and taking a ferry. Flights are not direct and ferry service to Venice requires the trip to Istria; not a problem as we wont' have seen it before. Am I missing something or should we just make the drive? We will have already driven from Slovenia through Croatia so it does entail some backtracking but c'est la vie!
That is one incredibly long drive (834 km). I would fly personally. Total of 1.5 hours flight time between Dubrovnik and Venice via direct Croatia Air Flight.
If I had the time, I might drive down the Croatian coast one way and back north through Bosnia in the other direction and then on to Venice. In fact, in 2015 I did much of that - down the coast to Montenegro, then back through Sarajevo and a few other Bosnia towns but only to Zagreb. However, check the car rental policies. Generally, it's best to rent the car and return it in the same country or you may face huge one-way drop fees for dropping in another country. I would either try to pick up the car in northern Croatia and drop it in the south say in Dubrovnik (and then fly to Venice) or drive back north to Slovenia via Bosnia and return the car there, then make your way to Venice by bus or train.
Volotea has cheap (currently $25-65) Dubrovnik-Venice nonstop flights about 3 days/week in June. There are daily nonstop flights from Dubrovnik to Rome, as well as some from Podgorica, both already tending to be more expensive than the first option; see www.skyscanner.com.