Scientists noticed that the atoms have internal structure. Although atom as whole acts as a neutral object (it is not attracted nor repelled to other charged objects) it does contain charged particles.

This leads us to the conclusion that there must be at least 2 charge types inside an atom and we refer to them as positive and negative.

Further investigation uncovered that negative charges, called electrons orbit around a tiny, extremely dense ball called nucleus. Nucleus contains positively charged particles called protons and neutral particles called neutrons.

As a matter of fact, electrons are indeed fundamental and believed not to contain any internal structure.