Bonnie is a word the Scots really do use for pretty, thus the root of this name, from the French bonne.
Gone With the Wind gave Bonnie a big push when Scarlett and Rhett used it for their daughter. Her full name was Eugenie Victoria, but the pet name came from the fact that she had "eyes as blue as the bonnie blue flag."
Bonnie's last moment in the limelight came in the late sixties with the film Bonnie and Clyde, about outlaw Bonnie Parker. Now after a long decline, it's finally showing new signs of life, perhaps thanks to the Bonnies in The Vampire Diaries and The Hunger Games, as well as a new miniseries about the 1930s-era bandits.