Is it because the freemasons made them so?
Indirectly, yes.
http://www.thevesselofgod.com/towardtheundivided.html"The word "hermaphrodite" is a conjunction of Hermes and Aphrodite, a union of the masculine and feminine aspects of God. The symbolism of the Hermaphrodite and its central significance to alchemy is well-known. Its importance to occultists in the guise of
Baphomet is likewise well-known."
"The well-known square and compass of Freemasonry is yet another symbol of the conjunction of masculine and feminine principles. The square is used to draw a square, a male symbol. The compass is used to draw a circle, a female symbol. The circle contained with a square thus represents, yet again, the same equilibrium of opposites."
The Fleur-de-Lys is the pre-eminent heraldic emblem of French royalty, and is said to represent a lily, symbolic of Davidic descent. While flowers in general symbolize the female reproductive organ, the lily is even more suggestive of a vulva than most. But unlike most flowers, the lily possesses a phallic rod which thrusts forth from its interior, making it uniquely hermaphroditic in its symbolism.