Zagreb is the best connected of Croatia's airports and will offer you the most options in terms of airlines and prices. Dubrovnik can be a good endpoint as it is at the southern tip of the country and you won't have to backtrack. The other airports would either involve back-tracking (Split) or aren't as well connected (Pula).
As you're planning your itinerary, also consider that you can usually get a relatively cheap domestic flight on Croatian Airlines which opens up the possibilities of where you fly in/out. You could even have an itinerary where you fly into and out of Zagreb without any back-tracking if you also have a one-way flight to Dubrovnik, and then work your way back to Zagreb. You might have to get a little creative if you need to keep expenses down.