Great question! We know electrons have a charge because they are essential in transporting electricity. Benjamin Franklin pioneered the study on electrical charge, and he arbitrarily (and most likely unknowingly) named electrons to have a negative charge. Later, Ernest Rutherford deemed the hydrogen atom to be the simplest element we know. He found through experiments that the nucleus contained the elementary particle now known as the proton. Since negative electrons orbit the nucleus, and to keep all the electronegativity at neutral, we know that the proton must have a positive charge. Finally, isotopes of different elements have different weight, but keep the same number of protons and electrons (and have very similar chemical properties). Thus, in order to accommodate this, a third fundamental particle called the neutron was introduced by James Chadwick to add to the mass of the element but not contribute to the charge of the nucleus.