There is no queen or the queen is not in power. Or, the queen is fairly reasonable, but not perfect.
All rulers, kings or queens, are just as bad.
Enforced: The show's hero backstory has him as an orphan. During his adventures he already found and fought his long-lost evil father, so writers want to use a long-lost evil mother. As she won't be appealing as a direct opponent, they go with the "Evil Queen" stereotype.
Lampshaded: "People are oppressed, and Black Guards look too sexy and stud. Must be an Evil Queen."
Exploited: In an attempt to halve the competition, a group of misogynist aristocrats (who are among those eligible to take up the throne) use the queen's tyrannical reign to justify why women should not be allowed to rule.
The queen is naturally mean-spirited, but forces herself to be nice since she doesn't want to come across as evil or oppressive.
Those around her dread the day of the princess's coronation and ascent to the throne because of this trope, but when the day comes she proclaims herself king.
A system is set up so that women are fairly, but just as strictly, evaluated before deciding who gets to rule the country.
"Yes, that's Queen Marianne. She's evil."
A Straw Misogynist states "She's a woman in power of course she's evil!" about the queen.
Conversed: "Why is the Queen always evil in these shows?"
Queens are all evil, but mainly because the society is so horribly sexist that mind-warping abuse is heaped on young women to the point that any one who gets into power is driven by a combination of vengeance and possibly insanity.
Alternately, she isn't quite as evil in comparison to your typical ruler of the period / locale, but she gets a bad reputation precisely because society is sexist and she's a woman—things that a male king could get away with are considered "atrocities" when she commits them because women are supposed to be gentle.
The queen's wickedness is part of the Machiavellian Magnificent Bastard traits that got her to the throne in the first place, given that it's a male-dominated medieval setting. A nicer woman would never have made it.
Or even in a society with gender equality, only a few women would prefer ruling the country, only to get ousted by that wicked woman, together with the rest of the men.