Although some people are attempting to dehumanize them recently, most people understand that ships are always female. They say it’s about feminine nouns in old languages, or Oedipus complexes if you’re into that sort of thing.
I totally understand how these theories arose, if nothing else, humanity is damn good at lying to itself, at making itself believe a lie to explain something otherwise inexplicable.
Because the ship that was male, the space ship that seeded humanity on this planet? That’s not one humanity likes.
Which I suppose actually is an Oedipus style issue, but a complete coincidental one, really…