Going to from Zagreb to Rome and back should be a one hour affair at most. This is the flight that I will be taking to advise my clients in the Italian capital.
Instead, the flight makes a stop in Split on the Dalmatian coast. Therefore, you end-up with two 45mns flights with a journey that can take 5 hours door to door.
The main problem is that in Split, you have to get off the plane and clear customs. Furthermore, strong winds (called “bura”) and fog can delay, or worse, ground the plane.
Below, the “Split” airport.