He doesn't know every reader, does he? I prefer people who could be either/or. It's more realistic that way. No one person is 100% evil or 100% good - if so, they'd be caricatures.
Also, if you write the "bad-guy" as
bad, you'll either have a 2D character or pantomime villain.
If you write from the POV of the antagonist, THAT CAHARACTER believes they are right. IF you are true to THAT character.
In the most recent Batman movie, Ras al Ghul believes what he and the League of Shadows do is for the good of mankind. He really sees himself as the good guy. He recognizes that what he does, how he achieves his goals, is outside the norm of society. Even recognizes that society would view him as a criminal, but within his own idealogy, he is simply more aware of the world than others. Drastic times require drastic measures.
He sees Batman as a weak fool. Someone who could be of great service to mankind if only he follwed the lead of the LoS.
When Batman stands up openly against him, Ras sees Bats as the enemy, clear and simple. Batman becomes HIS antagonist Someone who stands between him and his goal to save mankind from itself.
Depending on the complexity you wanted to work in, you could legitimately make Ras al Ghul a hero. He sees corruption and greed and evil. He has the power to thwart that and uses that power. How is he any different from Batman in that respect?
That's a movie, so in prose you have much greater room for subtlty and nuance.
Like PeeDee says, just write it the best you can, let some folks have a read, and if they all come back with the same issue (that they don't know who the hero is) you have a problem. If not, you don't.