Air Travel Public Health Emergency Protection Act This bill directs the Federal Aviation Administration (FAA) to authorize states, territories of the United States, and Indian Tribes to implement reasonable guidelines and restrictions to ensure the public health and safety of air passengers and the public. During a public health emergency such as COVID-19 (i.e., coronavirus disease 2019), the FAA must allow these governmental entities to enforce the reasonable restrictions on the boarding of any air passengers, including pre-board tests (e.g., temperature or other rapid check for any communicable disease which is the subject of the public health emergency) and related denial of boarding. The reasonable restrictions must be implemented at the expense of the air carriers. Additionally, during a public health emergency, the Department of Transportation must waive any grant assurance that conflicts with a reasonable restriction implemented by a state, territory, or Indian Tribe without an airport owner or operator submitting a request for such a waiver.