Transportation systems including air transportation play one of the most important roles in the economic and social development of any country. The effectiveness of the quality of control of such complex systems can be assessed according to various criteria, from the cost of developing infrastructure to the degree of satisfaction of the population with transport. The problem of assessing the quality of the air transport system for a passenger is considered. The proposed methodology is based on a pair of interrelated indicators, the so called «transportation standard indexes». The algorithm for the calculation of those indicators has been created, which is based on the schedule of domestic commercial flights. The methodology is implemented into a software module, that has been used to calculate the values of introduced indexes for both historical and hypothetical air flight schedules inside the Russian air transportation system.