When an ebonite rod is rubbed against a fur heat is produced due to friction. Since generation of energy is taking place it helps in transfer of electrons and charges are developed on the bodies.
Historically, the charge developed on the ebonite rod was given the name negative charge and is followed then onwards.
It is like asking why force is called force and not torque. It’s the nomenclature which was given in the past and is followed then onwards.
Hope this helps,