Passenger flow is an important planning factor in an air transportation system. However, forecasting segment (link) and airport flows becomes more complicated in a hub-and-spoke system since segment flows are the aggregations of route flows, and the number of routes increases with hubbing activities. This research develops an equilibrium model considering certain important characteristics of an air transportation system such as distance, airport delay, airline competition, and networks to predict segment and airport passenger flows from the viewpoint of the whole system. The major features of the model include (a) treatment of segment flows and airport delays as endogenous by considering the feedback of assigned segment flows and their impacts on airports; (b) reflecting the flexibility of air networks, a start with all links between all airports as the potential network and determination of the predicted network according to the equilibrium flows on segments; and (c) connection of key elements of the system so that it can evaluate the system impacts of some element changes. The model is demonstrated by applying it to the National Airspace System of the United States. Several characteristics of the model are also investigated. In addition, a policy experiment shows that improvement of an airport not only affects the airport itself but also changes the flows and performance of other airports - the model can be a tool for evaluating systemwide effects. Finally, the model's limitations and possible remedies are discussed.