Sir,

I read from one book that protons flow from higher to lower potential..Then in the case of a capacitor when we connect two plates to the battery source, then the plate connected to the positive terminal of the battery is at higher potential than the other plate...so protons must flow from higher to lower potential,and thus the one attached to the positive terminal of the battery should be negatively charged..But this is not the case..Please do correct me if i am wrong....

Charge on proton is equal to the charge on electron and also equal to atomic no, when this quantity put in an electric field, it flows from higher potential to lower potental.
the Capacitor, sometimes referred to as a Condenser, is a simple passive device that is used to “store electricity”. The capacitor is a component which has the ability or “capacity” to store energy in the form of an electrical charge producing a potential difference.
Electric current is due to flow of charge, either electron or protons.
So never confused that positive plate is considered to be at higher potential, its a conduction and induction process...

Good Luck............................................