I think it comes from a scientific term that means matched, or aligned. the idea is that your gender matches your body but to a lot of women that's really insulting as they believe that gender is the way you are socialised by society, which is why it changes over time and place. The transgenderists believe that gender is innate.
I have a female body and a personality which is my own, I don't believe in gender.
What really gets my goat is that language is Very Very Important to trans activists. Respect the pronoun of choice, do not talk about female biology, burn books that mention female biology, well, they broke into a library, intimidated the female volunteers and poured wine on the books but you get the picture. So, the Words we use must be policed lest we offend, but the trans activists, indeed it's common everywhere, rename women as cis which is so deeply offensive to many.
The term cis confirms their whole theory, that everyone has an innate gender. So it is like telling a non Muslim that she is a Christian, even though she doesn't believe in any god.