Again, I *really* hate to use Death Note as an example, but it's the most blatant that I can think of.
In Death Note, Kira/Light is the villain of the story, killing thousands of people. L and the collective Police forces are trying to stop him. L, as well as his successors, uh, N and M or whoever, have their own character arcs and are clearly 'the heroes', but the story isn't 'about them'. They aren't the protagonists, Kira is. The story is about all the shit that Kira goes through to kill all bad people. It's about all the fucked up shit that he does to himself and the people he loves in his struggle to Kill All Bad People (tm), whether he's right in his way of thinking or not. L, M, N, and the cops are obstacles that Kira attempts to overcome, and the story is framed in a "How will Kira avoid getting caught" manner.
Similarly, Thanos is very obviously the bad guy, but the story primarily follows Thanos in his goals of getting the Infinity Stones. We see the rest of the Avengers, and we see the things that they are doing to stop Thanos, but the story revolves around Thanos, making him the Protagonist.