In Germany during the Peasants’ War it the rainbow flag was a symbol of hope and change. In Italy it is affiliated with peace; you see a lot of houses with the rainbow flag draped on the balcony. In the Bible, the rainbow is a sign of God’s covenant with Noah and his family. Many of the liturgical colors happen to be rainbow colors: green, blue, purple, red and yellow (though technically it is gold in the liturgy). In 1994, Most Rev. Desmond Tutu and President Nelson Mandela described the new South Africa as the rainbow nation due to all colors being welcome after the end of the apartheid.
Should we be ashamed of the rainbow because of its current affiliation? No. I obviously love Rainbow Dash, one of the Mane 6 in My Little Pony: Friendship is Magic. I don’t see it as all as making her gay. Having rainbow-colored mane alone does not make a pony gay.