I mean, like the poster said, ships and stuff are generally considered feminine in nature (and there are things that are masculine in nature, but seeing as ships are the only thing I remember the gender of, I can't give an example). Atlantis is a ship. Thus usually, Atlantis is female, even if it's not described as sentient. I don't think it's a conscious effort or some kind of slight, but there's nothing wrong in deciding to make Atlantis male. ^.^