Protecting Railroad Operators, Travelers, Employees, and Communities with Transportation Security Act of 2004

Protecting Railroad Operators, Travelers, Employees, and Communities with Transportation Security Act of 2004 - Directs the Secretary of Transportation to complete a vulnerability assessment of railroad transportation that includes identification of vulnerabilities specific to the transportation of hazardous materials by railroads and of security weaknesses in passenger and cargo security. Directs the Secretary of Transportation to develop prioritized recommendations for improving rail security.

Directs the Comptroller General to study and report to specified congressional committees on the rail passenger transportation security programs carried out for rail transportation systems in Japan, member nations of the European Union, and other foreign countries.

Authorizes the Secretary of Transportation to make grants to railroad carriers, nonprofit employee organizations that represent railroad workers or emergency responders, hazardous materials shippers, owners of rail cars used in the transportation of hazardous materials, universities, colleges, and research centers, and State and local governments for reimbursement of costs incurred to prevent or respond to acts of terrorism, sabotage, or other railroad security threats.

Authorizes the Secretary of Transportation to make grants to Amtrak for: (1) fire and life-safety improvements to the tunnels on the Northeast Corridor in New York, New York, Baltimore, Maryland, and Washington, D.C.; and (2) certain systemwide Amtrak security upgrades.

Establishes a research and development (R&D) program to improve railroad security. Directs the Secretary of Transportation to develop and issue detailed guidance for a rail worker security training program to prepare front-line workers for potential threat conditions.

Sets forth certain railroad employee whistleblower protection requirements.

Amends Federal transportation law to require the Secretary of Transportation to develop and update a curriculum necessary to train public sector emergency response and preparedness teams, including standards for the training of persons responsible for responding to emergency situations during the removal and transportation of hazardous materials and high hazard materials. Prohibits a rail tank car containing hazardous materials from being transported or stored on rail tracks unless information identifying the tank car, the hazardous materials within such tank car, and response guidance is immediately available through Operation Respond Institute's technology or similar technology to local first responders in each location where the tank car may be located.