The Latin root cis means ‘on the same side’ (in contrast to the Latin root trans, which means across or beyond). Gender comes from the Latin genus – kind, sort or class. So, cisgender refers to a gender identity/presentation that matches (is on the same side as) one’s assigned sex, or someone who’s not transgendered. The word was created to be a complement to the term transgender, and as a better alternative to saying ‘biological’ or ‘genetic’ man/woman when distinguishing a non-transgendered individual.
Gender was historically used to simply indicate different types of things, and this has persisted in modern usage, to a degree. For example, connectors and fasteners used in electrical/mechanical trades are gendered male or female. The difference between older usage and these modern ones is that now, those assignments are made in direct analogy to genitalia — the piece with something that protrudes is male, while the piece with a corresponding hole/indentation is female. Gender is also used linguistically: some languages have grammatical gender that assigns a gender to every noun, not always in correlation with the meaning of the word.