Safe TRAINS Act

Safe Transit and Rail Awareness and Investments for National Security Act of 2004 (Safe TRAINS Act) - Authorizes the Secretary of Homeland Security to make grants to improve the security of public transportation systems (including passenger, commuter, and light rail) against acts of terrorism. Sets forth grant uses and requirements.

Directs grant recipients to submit to the Secretary their emergency response plan as well as a plan for conducting exercises for emergency response and public transportation employee training pursuant to guidelines published by the Secretary.

Directs the Secretary to: (1) develop and disseminate to appropriate owners, operators, and providers of public transportation systems (including public transportation employees), and Federal, State, and local officials, a report containing best practices for the security of public transportation systems; (2) develop a national plan for public outreach and awareness of measures the public can take to increase public transportation system security; (3) develop a strategic plan for the security of the Nation's public transportation systems; (4) execute in conjunction with the Secretary of Transportation, a Memorandum of Agreement governing the responsibilities of the Department of Homeland Security and the Department of Transportation, respectively, in addressing security matters for public transportation systems; and (5) establish National Transportation Security Centers at institutions of higher education to assist in carrying out this Act, to conduct research and education, and to develop or provide professional training of public transportation employees.

Sets forth certain whistleblower protections for employees or other persons who have commenced, testified at, or participated in, a proceeding to enhance public transportation security, or who have refused to violate or assist in the violation of any regulation related to public transportation security.