Say you have two atoms linked by a double bond. Things that are on opposite sides of them are on trans- sides of them. Things that are on the same sides are on cis- sides of them, and you modify the chemistry related words accordingly.

So when people were casting about for a word to make an analogy with transgendered/transsexual, cis- seemed like it fit just right for a lot of geekiness: the gender that your brain has is on the same plane, the same side, the same wavelength as the gender that your body has. The symmetry worked well.