I have a similar problem on the rear hatch around the window weather strip. Does this problem (rust) exist because of dirt and salt around the window or is it rust that was there and not removed? I have similar problem around wheel flares.
Usually caused be condensation/water sitting collected in an unprotected area (like floor pans/soggy carpet). Dirt/salt etc. just compounds the problem (like up in the fender wells
or behind the fender flares.