Why *do* they call this taxon gender?

Historically, gender had nothing to do with sex. The two concepts have become conflated in Modern English but in some languages the genders are, e.g., long thin objects, flat round objects, etc. In some languages nouns of different genders have different number names used when counting them.

The IE root is a word meaning to give birth, beget, but the meaning had shifted to kind before it came to be applied to the grammatical concept. Das Mädchen is neuter because all diminutive words are neuter in German.