Many of today's Church symbols come from the Emperor Constantine when in 325 AD began transforming the pagan way into the new found religion of the Roman Empire.
He started by transforming the pagan temples into Christian Churches. It was to him easier to change the sign above the door saying "Temple of the Sun God" to "Our Holy Church" instead of changing the entire building.
One thing that was in these Pagan temples to the "Sun God" was stained glass windows. These windows were a symbol of the magnificent glory of the sun.
And it caught on with Christianity. Today many Churches love their stained glass windows with their pictures of Jesus and Mary on them. Not ever questioning the building in which they attend worship.
