Why do things have colour? (reflect certain wavelengths of light) Why does something like an apple, which has many different types of atoms and molecules in different arrangements put together in a complex manner, reflect only certain wavelengths of light, instead of being a mess of colours for each individual type of atom and molecule?
 A: An object generally does reflect light in a multitude of wavelengths, just some more than others.  In an apple, the color of the skin is determined by the balance of pigments it contains.  In a red apple, the red pigment is most prominent, but green and yellow pigments are also present and reflect those colors of light in smaller amounts.
Our vision isn't precise enough to be able to differentiate the light emitted by individual molecules, so we instead see the average color reflected by a group of molecules.  Because of that, the whole surface can appear to be only a single color even if the color actually varies on the molecular level.
It's similar to how we can perceive a smooth, many-colored image on a computer screen despite it being made of separate units that emit only three colors. The light sources are so small and close together that the eye can't tell they're separate.
A: As light in the form of photons strikes an object, the photons interact with the electronic quantum states of the object, often getting absorbed by exciting the electrons of the object into higher energy states. Some of the energy gained by the electrons in this way will be converted into vibrations (temperature) in the object, which leads to emission of light in the infrared spectrum. Some of the energy will be converted back into photons as the electrons "jump" from a high energy state to a low energy state, which can lead to emission of visible light.
The size of that "jump" depends on a plethora of conditions, including the molecular structure of the object. Not just the individual molecules within the object, but also how they bind to each other, i.e. the whole structure of the object. And the color of the emitted light will reflect the size of the "jump". So if different objects have different molecular structures, and therefore different sizes of "jump" available, they will emit light in different colors.
This light is almost never just one frequency, but a sum of many frequencies that combine into mostly green, mostly purple, or whatever. One of the great qualities of lasers is that they are designed to only emit a single frequency (and phase, but that is for another time), which is achieved by highly controlled absorption and emission of light inside the laser.
So an apple, complex and organic as it is, has a color that is the sum of all the emitted light from the electronic states, and as the structure of the apple changes with e.g. rot, the color changes as well, as the balance between the emitted frequencies shift. I hope that answers your question.
