Rural Hospital Protection Act - Amends title XVIII (Medicare) of the Social Security Act to direct the Secretary of Health and Human Services (HHS), in determining reasonable costs for reimbursements to critical access hospitals (CAHs) after January 1, 2004, to include certain health care related taxes as allowable costs. Prohibits any offset, in computing such costs, against tax assessments paid by such a hospital of amounts the hospital receives from a state, if the Secretary has not determined that a hold harmless provision, meeting specified criteria, is in effect with respect to the health care related tax.