The correct explanation for how a rubber rod becomes negatively charged through friction is:
It is rubbed with another object, and electrons move onto the rod.
When two different materials are rubbed together (a process known as triboelectric charging), electrons can be transferred from one material to the other due to differences in their electron affinity. In the case of rubber, when it is rubbed with certain materials (such as fur or wool), electrons are transferred to the rubber rod, giving it an excess of electrons, which results in a negative charge. Protons, which are located in the nucleus of the atoms and do not move freely, remain stationary. Thus, the negative charge of the rubber rod is due to the gain of electrons.