Piracy doesn't equal lost sales. Those who pirate the game do so because they either lack the money to buy it, or are curious about the game, but due to the lack of a demo or other trial mechanism, need to vet the game.
$40 for an independent puzzle adventure game is pretty steep. Yes, Portal 2 was $60, but it had the marketing power of the first Portal, EA's publishing support at retail, as well as two storylines, Steam cross compatibility, and more.
The Witness has almost no marketing power aside from Jon Blow's name and the chance that somebody remembered that he made Braid eight years ago outside of the hardcore audience, such as the browsers of this forum.
I'm sure it's a polished, mechanically sound experience, but there are a lot of factors against it being a smash success.