Fluttershy is a Dragonborn.
 Long time ago a prophecy was told to the Dragons of Equestria, speaking of a being yet to be born who would have a dragon soul and the power to destroy the race of Dragons forever. Now, while some of the dragons went out hunting for this being others were a bit wiser and instead asked the Vanquishers of Discord, Princess Celestia and Princess Luna, for help.

They came up with an arrangement; Luna and Celestia would use the Elements of Harmony to ensure that the Dragonborn would be one of their pony subjects, thus making it much easier to find and guide them. In return for mitigating the Dragonborn threat, the Princesses extracted a pact from almost all the dragons of Equestria that stopped the violent hunts and treasure raids that the draconian race had been inflicting upon ponykind.

The last part of the deal was the gift of a dragon egg to the Royal Sisters, and egg that would be hatched by the rightful Heir of Princesses, an egg who would grow up to be the acknowledged Ruler of all Dragons in Equestria (Which turned out to be Twilight Sparkle and Spike.)The young dragon would be under the guardianship of the Heir and would learn the culture and ways of the more peaceful and organized ponies.

With the Dragonborn backing the Royal Sisters and their Heir, and the Heir protecting and supporting the future Draconian Monarch, the goal was an eventual strengthening of the ties between the two races and the foundation of the first peaceable Dragon Kingdom.