We do not see individual protons or electrons directly with our naked eyes because they are subatomic particles and are much smaller than the wavelength of visible light. Our eyes are sensitive to light, which is composed of photons, and they interact with objects of similar or larger size than their wavelength.
However, we have experimental evidence and knowledge about the presence of electrons in atoms. The behavior and properties of electrons have been extensively studied and understood through various scientific experiments and theories.
The interaction of electrons with light and other particles is studied in fields such as quantum mechanics and spectroscopy. These studies have provided detailed information about the behavior, energy levels, and interactions of electrons in atoms.
The way we "see" atoms is through indirect methods, such as using electron microscopes or techniques like scanning tunneling microscopy (STM). Electron microscopes use beams of electrons instead of light to image atomic structures, allowing us to visualize the arrangement of atoms and even individual electrons.
In summary, while we cannot directly see individual protons or electrons with our eyes, we have gathered significant evidence and understanding of their presence and behavior through scientific investigations and experimental techniques.