Small Airport Relief Act of 2009 - Requires the Secretary of Transportation for FY2011 and FY2012 to apportion amounts for airport planning and development and noise compatibility planning and programs to sponsors of primary airports based on the number of passenger boardings at the airport in calendar year 2008 if it had: (1) fewer than 10,000 passenger boardings in the calendar year used to calculate the apportionment for that fiscal year; and (2) 10,000 or more passenger boardings in calendar year 2008.