The practice of viewing queens—particularly those who exercised political power and weren't just consorts—as evil goes back to a time when monarchies were more common. It has played heavily into the lives of real life queens in history—even if their rule might have been decent or competent.
Sexism
The idea that "only a fool would want to be ruled by a woman" meant many queens tended to be viewed with suspicion or contempt by their male underlings. This is particularly true if the queen's manners and sexual habits
were similar to those of powerful men.
Xenophobia
Thanks to
Altar Diplomacy, queens were very often foreigners to the countries of which they became queens. They therefore became victim to xenophobic prejudices.
Especially if there arose a conflict of interests or—even a shooting war—between the queen's native and adopted countries.
