Biofuels Air Quality Act - Amends Federal highway provisions (with respect to the congestion mitigation and air quality improvement program) to direct the Secretary of Transportation to consider the extent to which a proposed project or program reduces sulfur or atmospheric carbon emissions.

Allows States receiving minimum apportionments to use funds under the program for renewable fuel projects (specified below).

Modifies provisions regarding renewable fuel projects to expand coverage to include: (1) publicly and nonprofit (currently, limited to privately) owned vehicles or vehicle fleets; and (2) costs of renewable fuel, consisting of any fuel produced from grain, oilseeds, or other biomass (including biodiesel), that is used to replace or reduce the quantity of fossil fuel present in a fuel mixture used to operate motor vehicles, and installation of capital equipment necessary for the conversion of storage and distribution facilities to carry renewable fuels or renewable fuel blends.