The two kinds of villains - evil vs troublesome
Pixar films often feature two main antagonists - one benevolent and one malicious - Buzz/Sid, Princess/Hopper. Ratatouille has three main antagonists: one evil (Skinner), one benevolent (Linguini) and a third, Anton Ego. Ego isn't malicious the way Skinner and Muntz are, but I wouldn't call him benevolent either. He is the best kind of villain - a 'good' one.
You might argue that all villains have a value system that makes them believe their actions are right, and it's true. The differene is that uually these values are egotistical or perverted, and are rooted in hatred or joy in the pain of others.
"Good" villains have some altruistic motive within them. They may stand in the way of your protagonists, but they have an important function in their community, which they perform with strict integrity.
If I am perceived as a 'good' villain, and in my story, I am the protagonist, how do I change the perception to be a protagonist in ALL stories? Perceptions and branding matters.
If someone else is the protagonist, I will surely be the villain.