Rural Transit Improvement and Flexibility Act of 2009

Rural Transit Improvement and Flexibility Act of 2009 - Revises the apportionment of nonurbanized formula grants for amounts remaining after apportionment for grants to Indian tribes for public transportation on Indian reservations for FY2006-FY2009. Increases from 20% to 25% the amount of remaining funds to be apportioned to a state based on its land area. Decreases correspondingly from 80% to 75% the amount of remaining funds to be apportioned to a state based on population in nonurbanized areas.

Limits to 25% of its apportionment for a formula grant for a capital project for the special needs of elderly individuals and individuals with disabilities the amount a state may use for operating costs of equipment and facilities.

Limits a grant for operating assistance from exceeding 50% of the net operating project costs. Increases such limit to 62.5% of the government share of project costs in the case of a state containing nontaxable Indian lands, individual and tribal, and public domain lands (both reserved and unreserved), national forests, and national parks and monuments.

Requires the Secretary of Transportation to establish a pilot program for the award of grants to states to establish transit centers to improve transit service (buses and other transit vehicles) in urbanized areas with a population of less than 200,000 and in nonurbanized areas.