Who makes the rules in the U.S. department of transportation?

Congress is responsible for passing all laws. The President's Cabinet (which includes the Department of Transportation) is part of the executive branch of the government and has no authority to "pass laws", although they can and do propose ideas to members of congress and sponsor bills made by members of Congress. Also, after Congress passes laws regarding Transportation, the department is then responsible for carrying out, regulating, and enforcing the law. If members of the general public, or Congress believe that the Department is mismanaging the situation they can certainly propose new additions and changes to the existing law.