I've read all the answers, but nobody made any mention to one of my favorite villain protagonist: Lelouch vi Britannia.
He is from anime, so it's not expected to be found in the others answers, but I suggest you to watch the series (there are two seasons), he is the main character and the villain as well and you can get good references from them.
To put it simply, Lelouch is the throne heir of his country, Britannia, but for unknown reasons his mother died one night and his sister, Nunnally, ended up disabled because the trauma, and because all of this their father, the king of Britannia, sent his children (Lelouch and Nunnally) to Japan, the last conquisted country by the empire.
Lelouch grows as a normal student hiding his true identity as a Britannian prince, he is a genius and knows how to manipulate people and what is more he receives (this is related with the plot) a power to command whatever order to anyone just for looking directly at their eyes, what gives him a great chance to accomplish all his objectives. In the beginning Lelouch only wants to know why his mother died and take revenge for his father for doing nothing about it, and for sending him and his sister to exile. As result he used a false identity as Zero and established a criminal organization with japanese people (they wanted to recover their country, but Lelouch used it in his advantage) calling it justice against the empire, but in the end his methods ended up killing innocent people, like families of his dearest friends. During the series you see how his sense of justice to make a happier world for Nunnally got more and more rotten, until the point that he doesn't care who dies for taking revenge of his mother and sister disgraces, and at the same time he is fighting his best friend, a Japanese boy who is one of the best soldiers of Britannia.
I don't know about the plot of your stories, but there must be a good reason to turn your main character into a villain, not hating the others characters is enough, we can have different opinions but we can respect each other. In the case I'm talking about a character who wanted a happier world ended up corrupted by a lot of despair and even so, he saved the world. There's a variety of villains you can choose, not only being the evil one because he hates everything or because he simply enjoys doing evil, there can be villains like Lelouch who wants justice, others can pursue their personal dreams by harming people (in this case, they don't have any other option), or to take revenge for a loved one who was not recognized and forgotten by injustices, or even characters who are good as anyone but against their will they become the more evil characters for being saved again, they can be the main villains but they can be good as well.
In my personal opinion the last ones are the best, because in the end they are good people who does evil by stronger reasons. I hope this helped a bit!
And if you want more detailed examples of evil protagonist/characters with those profiles, here I leave some I like a lot:
- Lelouch vi Britannia from Code Geass
- Altair from Re:Creators
- Celestia Ludenberg from Danganronpa
- Nagito Komaeda from Danganronpa
- Orchid from Maplestory
- The Governor from The Walking Dead
- The main character from Fire Emblem Fates Conquest
- Tom Baldwin from The 4400
- Obito from Naruto