Doesn't the proton have the same charge as the electron? It's really late and I'm tired and can't think, but I'm clinging to that statement because I can't imagine how else hydrogen would be neutral. So that means the charge of the proton is just +e, whereas the electron is -e. Incidentally, the electron volt (and the proton volt, I guess) are units of energy, not charge. So your original question doesn't make sense. Scientists don't measure charge in electron volts in the first place.
The electron volt is the amount by which the energy of a particle with charge of magnitude e would change as it moved through a potential difference of one volt. The only difference between the two is that the electron would lose energy and the proton would gain energy (if the potential difference were positive i.e. if the electric potential *increased* by one volt between the starting and final positions of the charge). Vice versa if the potential difference were negative. Again, it's late, and I may have the signs wrong. You figure it out. Either way, it's irrelevant because we're just considering the *amount* by which the energy changed and using that as a unit of energy.