Do atoms have color?
Given the current scientific knowledge, there is no way to tell if protons, neutrons, or electrons (Which would be visible at an atomic level) Have color.
Atoms are simply just too small to be able to tell. As an example, if an orange were the size of the earth, the atoms in it would be around the size of marble. However, we know that pure elements, such as gold, do have color. And since elements are described as the smallest particle that has the same properties as the element, it may be possible that individual atoms reflect light, and thus have color. But as I said before, there is currently no way to know for sure.
Actually, if you look at it logically, atoms have to have color.
First off, consider that color is merely light radiation of a certain wavelength. Red, for example is 630-700 nanometers. The wavelengths that are visible to us are know as visible light. Visible light is only a very small part of the electromagnetic spectrum.
Secondly, we know that electrons can jump up or down from different orbits. When they go down they release energy (photon). This energy is in the electromagnetic spectrum and sometimes (possibly all the time) some of that energy lies in the visible light spectrum.
Hydrogen, for example, emits energy in red, blue, indigo and violet wavelengths.