What I think is : The protons are present at the centre of the atom with rotating electrons around it so when it is rubbed by fur the electrons get passed from the ebonite rod to the fur leaving the rod negatively charged. But in reality the rod is negatively charged Why ?
When you rub fur with ebonite rod, the chemical bond is formed between some parts of the the two surface. Rod has its electron more tightly bound than fur. So, fur donates electrons to the rod while electrons from rod won't come out. Due to excess of electrons in rod, it becomes negatively charged while the fur with lost electrons, becomes deficient of electrons. Thus, fur becomes positively charged.