Thanks to everyone for your tips to date.
We will be traveling from Venice to Ljubljana by train and need to rent our car either at the station or in town and will return it at the airport. Any recommendations on which company to go with?
For the best price, use EconomyCarRentals, Kemwel, AutoEurope, etc. to check prices - you won't know the name of the car company in some cases until you have booked (but all of those brokers should give you refundable reservations up til 48 hours before car pick-up, so you can always cancel if you find the pick-up location isn't ideal.)
I rented from Sixt in Ljubljana a few years ago. Their office is right at the Ljubljana train/bus station so super convenient. I'd rent from Sixt again if their price was competitive.
Are you really taking a train from Venice to Ljubljana (through Austria?). It would save a lot of time to take a shuttle service like GoOpti or DRD. (If you use DRD, it is essential to contact them in advance and perhaps buy tickets in advance. Don't show up at a stop and assume they will pull up a bus at a scheduled time - they aren't a conventional bus service.) I haven't used GoOpti but have heard good things.