Well, as per Disney, pretty much any feminine title except Princess is given to a nasty character.
Evil Queen in Snow White
Lady Tremaine in Cinderella
Queen of Hearts in Alice in Wonderland
Queen Jadis in Lion, Witch, and Wardrobe
Evil Queen in Willow (not Disney, but the association is there and her daughter, the princess, starts out evil and ends up good)
Maleficent in Sleeping Beauty (she's not given a title, but she certainly seems to "rule" over her many demonic-looking minions, while the good faeries have no underlings at all)
Ursula (is royalty of some kind since she references having lived in the palace before)
The other variation of this is that the Queen serves only to be mom/role model to the princess/prince... in these cases, often she's not even given a name beyond "the queen"...
The Queen in Bug's Life
The Queen in Tangled
Queen Clarion in the Tinkerbell movies
Queen in Sleeping Beauty
Queen Athena in Little Mermaid 3
Queen Sarabi in Lion King
Hera in Hercules
Due to their source material (classic faerie tales and legends) women in power are usually portrayed as dangerous or, the other side of the coin, motherly... with dangerous being far more common since men were often penning these old stories and found the idea of powerful woman to be intimidating. Thus the archetype of a "princess" is much more common. Disney is not truly to blame, they are just using what history had given them.
This being said, they have branched out with strong, non-princess female characters; Mulan, Belle, and I very interested to see the new Pixar flick Brave.
Thus, when Lauren Faust and her team decided to make Celestia and Luna princesses, rather than Queens or Empresses or what-have-you, they were merely choosing what most people deem to be a less-threatening title.
Or maybe I am reading too much into this.
Rose-who-did-her-senior-thesis-on-adult-themes-in-Disney-movies