I'm not sure if she really counts as a villain, but I am posting her anyways. Vriska Serket from Homestuck. She's not as bad as some people think her to be. She's actually a pretty sweet girl at heart.
Not to toot my own horn but... I like a character from some of my own stories, Crisanthe. The main reason is because she is only seen as a villan to those who don't follow her.
Let me give you some background: She was born in a country known as Rensi is a province known for its scientific achievements, known as Helina. Helina was once a proud and powerful nation until Rensi took it over about a thousand or so years ago. por 1805 Rensi had the world taken over. Then in 1995 a province known as Konssia had broke away because of the tyrany of the Emperor of Rensi. Konssia chose to close its borders. In 2012 a young revolutionary named Hide Yojiche started a revolution that overthrew the Rensian emperor and established a new Dynasty. During that revolution Crisanthe wanted some honour for her own people, the Helins and the other people of Fallandic decent (Which was nearly all of the Northern Rensian continent) and they started their own nation.
Rensians see her as sort of a villan because she started her own revolution that dividido, dividir what was the nation of Rensi in half, but all she wanted was something her people can call their own.