Cleaner, Secure, and Affordable Thermal Energy Act - Amends the Internal Revenue Code to: (1) allow a tax credit for residential energy property expenditures to convert a home heating system using oil fuel to a system using natural gas boilers and furnaces and biomass heating appliances; (2) allow bonus depreciation of property used to convert a home heating system; (3) allow the use of tax-exempt energy conservation bonds to finance conversions of fuel oil heating systems; and (4) extend through 2012 accelerated depreciation for natural gas distribution facilities.