The reasoning is simple: it’s just straight up transphobia. The term “cis” is just a neutral descriptor to pair with “trans” with no implication of being right or wrong. They’re mad at the existence of a term for the majority that doesn’t imply an insult to the minority.
Thanks. Another commenter pointed that out. They’re not really taking offense to the term so much as objecting to the concept of genders differing from biological sex. It’s awful.
There’s no reason to challenge the term otherwise. Cis is Latin for “on this side of” and trans is “across, beyond, or on the other side.” There’s really nothing objectionable about either prefix.