While influenza transmission is thought to occur primarily by droplet spread, the role of airborne spread remains uncertain. Understanding the beliefs and attitudes of infectious disease physicians regarding influenza transmission and respiratory and barrier protection preferences can provide insights into workplace decisions regarding respiratory protection planning. Physicians participating in the Infectious Diseases Society of America’s Emerging Infections Network were queried in November 2013 to determine beliefs and attitudes on influenza transmission. A subset of physicians involved in their facility’s respiratory protection decision making were queried about respirator and surgical mask choices under various pandemic scenarios; availability of, and challenges associated with, respirators in their facility; and protective strategies during disposable N95 shortages. The majority of 686 respondents (98%) believed influenza transmission occurs frequently or occasionally via droplets; 44% of respondents believed transmission occurs via small particles frequently (12%) or occasionally (32%). Among the subset of respondents involved in respiratory protection planning at their facility, over 90% preferred surgical masks during provision of non-aerosol-generating patient care for seasonal influenza. However, for the same type of care during an influenza pandemic, two-thirds of respondents opted for disposable N95 filtering facepiece respirators. In settings where filtering facepiece (disposable) N95 respirators were in short supply, preferred conservation strategies included extended use and reuse of disposable N95s. Use of reusable (elastomeric facepiece) respirator types was viewed less favorably. While respondents identified droplets as the primary mode of influenza transmission, during a high-severity pandemic scenario there was increased support for devices that reduced aerosol-based transmission. Use of potentially less familiar respirator types may partially relieve shortages of disposable N95s but also may require significant education efforts so that clinicians are aware of the characteristics of alternative personal protective equipment.