This dataset includes data for the thesis titled "Economics, analytics, and optimization of air transportation systems". We have included the numerical results in the dataset, including numerical examples for airport capacity expansion, benefits of flexible truck-drone collaborations, airline fleet decisions based on real demand data, and system state trajectory under controls. This thesis provides a comprehensive investigation of modern air transportation systems through an integrated analytical framework that combines economic theory and operations research. It offers valuable insights for different stakeholders in the air transportation system.