Highway Trust Fund Commission Act of 2003 - Directs the Secretary of Transportation to establish a National Commission on Future Revenue Sources to Support the Highway Trust Fund to investigate and recommend alternatives to replace the fuel tax as the principal revenue source to support the Highway Trust Fund (HTF) over at least the next 30 years. Directs the Commission to consider: (1) the ability to generate sufficient revenues to meet anticipated long term surface transportation financing needs; (2) the roles of the various levels of government and the private sector; (3) administrative costs; (4) potential taxpayer privacy concerns; (5) likely technological advances; (6) alternative transportation vehicles, including alternative-fueled vehicles; (7) the equity and economic efficiency of each option; (8) the flexibility of different options to allow various pricing alternatives to be implemented; and (9) potential compatibility issues with States' tax mechanisms.