We were on this cruise last year and flew home from Ljubljana Airport late aftenoon, think it was about 5pm. We travelled from Koper to Ljubljana by train about 9am, we then took a taxi from the railway station to the airport. We had enough time even though because of rail works the train was diverted and part of the journey was by coach. We lost no time as the arrangements by the rail company were very efficient.
Using public transport on a Sunday is a problem as there are fewer trains.
The ship docks early so we had no problem leaving, we were off the ship by 8.30 and took a taxi to the train station about 10 minutes away.
Check the train times online & buy your ticket at the station.
Might wave to you on the 29th as we will be in Koper again that day on a shore excursion.