Rental car for Istria

You want to structure it so that you pick up and drop off the car within the same country--otherwise there is typically a very large fee (several hundred is what I have seen). Could you instead travel Venice to Istria overland or by ferry (https://www.venezialines.com/), then drop the car within Croatia and take train or bus to Ljubljana?
Picking up in Pula or Rovinj, for example, and dropping off in Zagreb would not incur a significant fee.

The Zagreb-to-Ljubljana trip takes about 2-1/2 hours to 3 hours by train (infrequent) or bus, I believe. FlixBus is the biggest player in the bus market. GoOpti runs shuttles that are faster and somewhat more expensive.

I liked Zagreb a lot in 2015, but one of our Croatia experts has reported that many of the large museums in Zagreb are still closed due to earthquake damage. If any Zagreb museums are of major interest, it would be important to check their websites to determine their status. I found the Croatian Museum of Naive Art small but stunning; it's open Monday-Friday. The Museum of Broken Relationships--which I feared would be too silly--was also very enjoyable. It's open daily. I didn't check on the many other museums in Zagreb.

This link will take you to a Google page showing most if not all the Zagreb Museums.

Check bus routes from Istria towns to Ljubljana too--I am just only familiar with the Zagreb train route.

Thanks for the replies. We plan to return the rental back to the same place where we pick it up. We have Eurail passes and will be going through a total of eight countries including the detour to Istria. Italy, Slovenia, Hungary, Austria, Czechia, Germany and Belgium. The rest of Croatia and the other countries in the region will be on another trip, hopefully. Thanks again...

You could take the train from Ljubljana to Rijeka and rent a car there and drive to Istria - that's what I did a few years ago. (There is train service to Pula too which would get you closer, but it's a much longer train ride with connections whereas the train to Rjeka is direct, and it's an easy drive to Rovinj or Pula from there. (It is about a 15 min walk from the Rijeka train station to the harbor where I picked up my rental car; you could take a bus or taxi or Uber there from the train station, though I just walked.) Not sure where you were planning to go after that. Obviously you could rent the car in Ljubljana and just drive to Istria and back.

Imo just rent a car in Ljubljana and make sure you can cross the border with it and go that way

We tookFlixBus from Rijeka to Ljubljana and while it was fine, I think it just adds more unnecessary complexity and time to take a slower mode of transport to trieste or Rijeka etc. and rent there.

The bus is kind of painful given the distance travelled and the train isn’t all that much better between Ljubljana and Zagreb. Imo I’d much rather drive to Pula, Labin, Rabac, and then to Opatija/Rijeka and loop back around to Ljubljana from there than go to Zagreb and head back this way.

We just drove much of these areas in November and the drive itself between Opatija and Labin along the coastal road are worth renting a car for imo.

Thanks to all those who replied.. . Very helpful.

Car rental in Trieste seems perfectly fine. You can pick-up and return the car in Trieste and do your loop through Istria and you may include Škocjanska caves.
In April there seems to be a daily direct train in the evening from Trieste to Ljubljana.