Transit System Flexibility Protection Act of 2011 - Authorizes the Secretary of Transportation to make grants for the operating costs of equipment and facilities for use in public transportation systems as follows: (1) not exceeding 50 percent in systems that operate 75 or fewer buses during peak service hours in an urbanized area with a population of at least 200,000, and (2) not exceeding 25 percent in systems that operate a minimum of 76 buses and a maximum of 100 buses during peak service hours in such an urbanized area.