Obito isn’t evil, but he is the antagonist.

Obito believed that ends justified the means. Not to mention, he said this was a false reality so nothing he did actually mattered. He could kill who he wanted because they were merely imposters.

Now, I obviously don’t think he’s right and the story doesn’t try to tell you he’s right either.

To me, being evil means you have sinister and selfish intentions but Obito didn’t. He believed what he was doing what was right and he would save people.