Re: Why are things transparent?

In the long form of your question I thought I detected that your picture of 
the interaction of light with matter involved light slipping through things 
despite the fact that there were atoms and molecules in the way.  Somehow, 
because of some special arrangement of the atoms or because they were not enough 
of them, the light manages to get through. 

Let's just clear the decks a little also.  By "transparent" we usually mean that 
there is no interaction with light.  Absorption is one type of interaction.  
Scattering and reflection are the other major interactions.  Both would mean a
material was not transparent, though if scattering is weak we sometimes call 
things "translucent".  I am going to limit my answer to absorption.

It may be better to look at the question another way and ask:  Why should atoms 
and molecules absorb light?  

We need to look at the absorption process itself.  To do so we must appreciate 
what light is and we can only do this by seeing how it behaves.   We describe 
light as being made up of photons, small packets of energy travelling literally 
at the speed of light!  Sometimes their behaviour can be explained by imagining 
them as little particles.  I get the impression that you are imagining a beam of 
light being made up of particles of light being fired at things and wondering 
why with some materials, all the particles manage to get through despite the 
atoms or molecules in the way.  Another way to describe light is a combination 
of an oscillating electrical and magnetic field.  That's why we refer to some 
types of radiation as electro-magnetic radiation.  

Light is the electro-magnetic radiation whose wavelengths are between about 
400nm and 700nm.  We can work out the amount of energy a photon has from its
wavelength; the shorter the wavelength the more energy.

How does light, that is a transient oscillating electro-magnetic field, interact 
with atoms and molecules in its path?   All the electrons in atoms and molecules 
occupy "orbitals"  or regions of space outside the positively charged nuclei 
which keep the electrons trapped.  We call them orbitals rather than orbits 
because they are not simple circular of elliptical paths like the planetary 
orbits but are often odd shapes.  These shapes are explained well if we 
recognise, as De Broglie did originally in 1924, that electrons have wave-like 
character in the same way that photons do.   The difference is that the 
wave-lengths of electrons are very much smaller than that of light. 

Each of the electrons occupying the orbitals in an atom or molecule has is at a 
lower energy that it would have if it were not trapped and the orbitals have 
different energies according to how close they are to the nuclei.   The 
electrons usually occupy the lowest energy orbitals leaving higher energy 
orbitals unoccupied.  However, when the disturbing influence of a photon comes 
along, when certain conditions are met, an electron may gain the energy of the 
photon and jump into an orbital with a higher energy state.  The photon is 
"absorbed" in this process and we say that the atom or molecule is now in an 
"excited" state. 

Unless this process occurs (or scattering or reflection as I have said before), 
light will pass by unaffected.  If it does, we will see the effects as a 
reduction in the amount of light passing through the material.  Usually the 
probability of absorption depends on the  wavelength of the photon (the 
availability of a higher level orbital corresponding the an energy change equal 
to the energy of the photon) and so the absorbing material appears to be 
coloured.  If for example all the photons between 400nm and 500nm were absorbed 
the material would be yellow in appearance.  If the absorbing range is 600nm to 
700nm the colour is turquoise or "cyan".

You may wonder what happens to the excited states.  Several things are possible 
including the almost immediate re-emission of a photon but usually the energy 
acquired is converted to vibrational energy or heat.

A friend recommended a book to read by Richard Feynman called "The Strange 
Theory of Light and Matter".  I'm going to take a look at it myself.