Railroad Carriers and Mass Transportation Protection Act of 2004 - Amends the Federal criminal code to rewrite provisions prohibiting acts of destruction and violence against trains, railroad equipment and structures, and the mass transportation system to: (1) correspond with current prohibitions against acts of violence against the mass transportation system; (2) apply such provisions to acts committed knowingly (currently, willfully); and (3) add as an aggravated offense the commission of such prohibited act under circumstances in which the railroad on-track equipment or mass transportation vehicle was carrying high-level radioactive waste, spent nuclear fuel, or specified hazardous material.