D. Ernest Rutherford
After the discovery of the electron, some scientists started hypothesizing that there had to be some sort of positive charge in the atom that balances it out. When Rutherford discovered the nucleus of an atom, people realized that positive charges existed inside that nucleus. It's hard to point out just one scientist who discovered protons, because it was really a group effort of many scientists, but the most popular scientist became Rutherford, he also named the proton.