Rural Provider Equity Act of 2003 - Amends title XVIII (Medicare) of the Social Security Act (SSA), the Public Health Service Act, and other Federal law with respect to rural health care, especially: (1) physician reimbursement; (2) rural health clinics and community health centers; (3) home health services and hospice care; (4) air and ground ambulance services; (5) mental health care accessibility; and (6) rural health services research.Amends SSA title XVIII to provide for coverage of marriage and family therapist services and mental health counselor services under Medicare part B (Supplementary Medical Insurance).Amends the Internal Revenue Code to exclude from gross income any loan payments under the National Health Service Corps Loan Repayment Program.