You’ve got two towels made from the same material, except one is red and the other is blue. What, at the smallest possible level, is happening on the towels that makes us see them as different colors?
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You can safely ignore the towels and go to the dye molecules. Dye molecules are chosen because their chemical structure leaves a gap in electron levels that corresponds to energy levels in the visible light range. https://en.wikipedia.org/wiki/Dye
Dye molecules have color because they absorb certain other colors of light. So more or less when a red dye is hit by white light (which is made up of the other colors of the rainbow), only red comes back.
They absorb different colors because of their molecular structure. Different colors of light have different amounts of energy in each photon. The electrons in a molecule have a set of levels they can be. If a photon hits a molecule that matches its energy, it can be absorbed. It’s like if you can only jump to another stair step if you hear the right musical note, because the pitch you hear corresponds to how high you can jump, and you can’t jump over and just fall back down.
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