"she" is absolutely proper English for a ship or boat, with a long history of use continuing into the present day, and many dictionaries also list a definition of "thing, especially machine" or something like that, though for non-ship/boat things the use of "she" is rather less common.
"It" is unambiguously the correct pronoun to use for a car. I'd really challenge you to find a native English speaker who would think otherwise.
I would argue a computer program is no different than a car.