Hi Tanya,
A few years ago my wife and I did a similar itinerary. We flew into Venice then took the train to Ljubljana, rented a car there for a few days, then train to Zagreb and on to Split. Then ferry down the coast ending up in Dubrovnik where we flew out of - great way to go without any backtracking.
In hindsight, we would have loved to have done a lot of this by car. The roads are very good in Slovenia and Croatia and the traffic is light. Also, the lakes are difficult to get to without a car. If you have ever driven in a foreign country you will probably find these countries to have easy driving. The Italians of course are a bit crazy on the road, but you won't be in Italy too long.
Are you sure that you can find a car rental company that will allow you to do what you want to do? If not, you could do what we did and rent a car in each country. We actually tried to change plans mid-stream and rent a car in Zagreb to drive down to Dubrovnik but they were all sold out.
If you want any more tips from our trip I would be happy to talk with you.
Cheers