Air transportation networks are being disrupted with increasing frequency by failures in their cyber- (computing, communication, control) systems. Whether these cyber- failures arise due to deliberate attacks or incidental errors, they can have far-reaching impact on the performance of the air traffic control and management systems. For instance, a computer failure in the Washington DC Air Route Traffic Control Center (ZDC) on August 15, 2015, caused nearly complete closure of the Centers airspace for several hours. This closure had a propagative impact across the United States National Airspace System, causing changed congestion patterns and requiring placement of a suite of traffic management initiatives to address the capacity reduction and congestion. A snapshot of traffic on that day clearly shows the closure of the ZDC airspace and the resulting congestion at its boundary, which required augmented traffic management at multiple locations. Cyber- events also have important ramifications for private stakeholders, particularly the airlines. During the last few months, computer-system issues have caused several airlines fleets to be grounded for significant periods of time: these include United Airlines (twice), LOT Polish Airlines, and American Airlines. Delays and regional stoppages due to cyber- events are even more common, and may have myriad causes (e.g., failure of the Department of Homeland Security systems needed for security check of passengers, see [3]). The growing frequency of cyber- disruptions in the air transportation system reflects a much broader trend in the modern society: cyber- failures and threats are becoming increasingly pervasive, varied, and impactful. In consequence, an intense effort is underway to develop secure and resilient cyber- systems that can protect against, detect, and remove threats, see e.g. and its many citations. The outcomes of this wide effort on cyber- security are applicable to the air transportation infrastructure, and indeed security solutions are being implemented in the current system. While these security solutions are important, they only provide a piecemeal solution. Particular computers or communication channels are protected from particular attacks, without a holistic view of the air transportation infrastructure. On the other hand, the above-listed incidents highlight that a holistic approach is needed, for several reasons. First, the air transportation infrastructure is a large scale cyber-physical system with multiple stakeholders and diverse legacy assets. It is impractical to protect every cyber- asset from known and unknown disruptions, and instead a strategic view of security is needed. Second, disruptions to the cyber- system can incur complex propagative impacts across the air transportation network, including its physical and human assets. Also, these implications of cyber- events are exacerbated or modulated by other disruptions and operational specifics, e.g. severe weather, operator fatigue or error, etc. These characteristics motivate a holistic and strategic perspective on protecting the air transportation infrastructure from cyber- events. The analysis of cyber- threats to the air traffic system is also inextricably tied to the integration of new autonomy into the airspace. The replacement of human operators with cyber functions leaves the network open to new cyber threats, which must be modeled and managed. Paradoxically, the mitigation of cyber events in the airspace will also likely require additional autonomy, given the fast time scale and myriad pathways of cyber-attacks which must be managed. The assessment of new vulnerabilities upon integration of new autonomy is also a key motivation for a holistic perspective on cyber threats.