I've been saying this since the movie came out almost 20 years ago and I saw it in the theater. Paul Thomas Anderson goes out of his way to show you that Plainview has earned his money. He even shows a scene where Plainview, with a broken leg, drags himself across the desert until he gets to the next town. When he gets to the next town, he still holds his head up to make sure the men counting his silver aren't cheating him.

Plainview is the one who understands oil drilling. He's the one who has the means and the knowledge to properly utilize the Sunday ranch. There are a few parts where Plainview does bad things. When he turns to H.W. and says "We'll give them quail prices." That was bad. He kills that man because he was pretending to be his brother.

And yes, at the end, Plainview shouldn't have bashed Sunday's head in with a bowling pin, but I think the real message that Anderson is trying to convey is that religion is the true enemy.