The air transportation system connects the world through the transport of goods and people. However, operational inefficiencies such as flight delays and cancellations are prevalent, resulting in economic and environmental impacts. In the first part of this article, we review recent advances in using network analysis techniques to model the interdependencies observed in the air transportation system and to understand the role of airports in connecting populations, serving air traffic demand, and spreading delays. In the second part, we present some of our recent work on using operational data to build dynamical system models of air traffic delay networks. We show that Markov jump linear system models capture many of the salient characteristics of these networked systems. We illustrate how these models can be validated and then used to analyze system properties such as stability and to design optimal control strategies that limit the propagation of disruptions in air traffic networks. Expected final online publication date for the Annual Review of Control, Robotics, and Autonomous Systems, Volume 4 is May 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.