I think Vergil certainly saw what he was doing as good. But he went about it in the wrong way.
I guess it depends on the player whether Vergil was doing the right thing or not. In my opinion, none of the characters (except maybe Kat) ended the game being 'good'.
Mundus enslaved mankind because he believed they needed saving from their own violence and greed when they were allowed freedom.
Vergil saw Mundus as a tyrant and wanted to free the humans. But Vergil also wanted to fill the void left with Mundus' defeat because in his opinion all humans knew was control. If they had freedom, they would not know what to do with themselves, and for this reason Vergil sees them like children who need him to rule.
I guess with Vergil, it also stemms from what he said was a lack of control in his life, which is why he turned to computers and hacking. So controling humanity would be the ultimate way of having control in his own life.