Can anyone tell me if these buses run 24 hours. I arrive late in the evening and would prefer to take the bus into the city.
Thanks

I you will be fine. From the Zagreb Airport FAQ:
"My flight is schedulled to arrive at 22:15. I wonder if I can use any public airport bus to the city center?
Yes, the scheduled bus shuttle "Pleso prijevoz" is operating in both directions between the main bus station in Zagreb and Zagreb Airport. This shuttle service operates in scheduled intervals up to 20:00 hours each day, however it is also organized in such a way that it follows the arrival of all scheduled traffic landings at Zagreb Airport.
More information available at: How to find us? "
http://www.zagreb-airport.hr/Frequently-asked-questions-149.aspx