Literally just means "not trans." Opposite prefix.
Observe here the genderologists attachment to binaries. Everything is X or not-X.
Genderologists are obsessed with binaries in a way that the GC crowd are not - we know that things are not denoted by their opposite. Women are not "not-men".
This is akin to religions, which often have their own terms for non-believers - gentile, kaffir... People who don't subscribe to the religion are generally not going to be terribly happy with being described like that - even if it's objectively true that they're a nonbeliever - favouring one particular religion's term for them.
Genderology is a bit more complex in that you have the priest class - those who believe they have a "different" gender, then the lay people - those who believe in the religion but believe/assume they have a "matching" gender. So the "opposite" term here is doubling up - it means "not a priest" inside the religion, but they also extend it to nonbelievers.
Maybe it's more like a caste thing - everyone outside the religion is treated as if they were the lower caste of the religion, despite not being part of it.
It's this dual meaning of "cis" that's the problem - it's simultaneously applied to "people who believe they have a gender that matches" and "people who don't believe in gender". If the definition was made super precise - "people who don't believe that they have an inner essence contrary to their sex" - making it more atheist-like - you might get away with it, but that's not a definition you ever see, and it's not how it's used in practice. The definitions seem to have the "gender is a thing" assumption built in.
It's worth noting that we are objecting to being called "cis" because genderologists call non-believers cis. If they called us "trans" we'd be objecting to that too. (Actually, there is some transing of the dead happening, and yes we do object).
It's not using that specific word it's classifying us within your binary. We reject your cis/trans binary. It's a social construct that does not correspond to material reality or our lived experience (as the cool kids call it these days).