Road infrastructure in Iran can go beyond your expectation. If you’re coming to Iran with a tour, you can be sure all of transport between cities is provided for you, whether by train or planes, couches (car/bus/middle bus/van).
However if you’re a freelance traveler, you can easily find transportation vehicles from city to city. For short distances between cities or in any case that you want to go from a city to a smaller one or to a county/village there’s always taxi. Make sure you’re taking yellow taxis which are licensed ones.
For farther distance you can still use taxis but it will cost more. So you can share it or you can take buses (mini/middle/regular). For the most important cities in Iran (regardless of distances between them) you can always find buses, during both day and night.
One of the other ways to explore Iran is going by train. Railways of Iran work efficiently and night train is one of good options to travel between far away destinations. Meals including breakfast, lunch and dinner are available in these trains or you can carry on your own.
Aviation services and planes are also a good option if you’re not interested to sitting in a road vehicle for a long time. Despite of being a large country, the longest flights between most popular cities as touristic destination are no longer than 2 hours.