 Governor Ehrlich appointed Flanagan to Maryland Secretary of Transportation.In this position, Flanagan managed the Port of Baltimore, Baltimore Washington International Airport, the Maryland Motor Vehicle Administration, the various transportation entities, such as the MARC Train, the Baltimore Light Rail, the Baltimore Subway, and the Maryland Transit Administration.During Flanagan's tenure as Secretary from 2003 to 2007, Maryland obtained approval under the National Environmental Policy Act to begin construction of the Inter-county connector as a state of the art, congestion managed highway by developing a new environmentally sensitive design after two prior rejections by the EPA in 1983 and 1997.