Because charge is quantised. You can't1 get less charge than the charge of one proton (or electron). Therefore there's no way for charge to flow from a single proton (or single electron).
In your macroscopic example it's not charge itself that is moving, but the charged particles (most likely electrons) that are moving between the bodies.
1 Ok that's not true. Protons and neutrons are made of quarks, which have either positive or negative one third or two thirds the charge of a proton, but the force binding them (the Strong force) is so strong they cannot2 be exchanged. A proton is defined by quarks that sum to a total charge of 1 and a neutron by quarks that sum to a total charge of 0.
2 Ok, that's not true either. Sometimes sea quarks can hadronize and escape, and all sorts of other complicated things that only happen in high energy physics.