I travel to Zagreb Pleso airport about 2-3 times a year and have never had bad experiences. I like going by bus to/from the arrival hall because it is much different than all the large airports and it has its charm. When the weather is bad the bus parks close the aircraft's stairway and mostly the stairways have a roof on it so the change of getting (very) wet is minimum.
Waiting at passport control is never long. The airlines have special "online" check-in desks so if you already chose your seats before departure you never have to wait long in line. A good advice is to phone your airline a few days before departure and maybe they can already assign you seats in the aircraft. Most of the airlines have that service. There's also a very good bus transportation to/from the airport from main bus terminal and very inexpensive 30Hkn/€3,60. You can buy tickets at the main bus terminal or on the bus itself. It departs every 30 minutes, starting at 6:00am, and terminal is easy to reach by tram.

A few other things worthy of note:
The airport has no jetways, so boarding/deplaning is via bus to the parked plane on the tarmac. Be prepared to get wet in the rain, to be cold in the winter, and to steam on the bus in the summer (no A/C!). Elderly or physically challeneged passengers may have problems.
Access to the departure terminal can be challenging, as it involves going up one level after clearing security and then down another level, both on escalators that are not always operational.
On arrival, all luggage is passed through scanners, so getting through may take some time.

Quite nice small airport.
Expect family atmosphere and laid back attitude. It can improve tremendously. The town fathers are planing to build a brand new one untill 2010. Traffic is rather low, so there are no long lines, hectic and stress.
Duty free shop is very modest, poore almost.
Toilets are clean and modern.
Coffee shops and a restaurant on the first floor are full of cigarette smoke.