Popularity isn't always a good thing
The Witness is very popular this week, but popularity and revenue don't always correlate directly. There's a whole subset of people out there who prefer to get their games through nefarious, illegal means and The Witness has found itself as a prime target.
According to lead creator Jonathan Blow, The Witness is the top-pirated video game on a "certain popular torrent site" which he declined to name. Blow lamented that "Unfortunately, this will not help us afford to make another game." In a subsequent tweet, Blow expressed the slightest of silver linings in that more people will be able to play it. Still, that consolation doesn't help his bottom line or his ability to start another project.
It's not a new phenomenon for Blow who stated that Braid, his first game, saw the same degree of illegal downloading. It's enough to make him consider some sort of DRM protective measures for whatever he does next, although Blow said he "[Doesn't] like DRM because [he thinks] people should have the freedom to own things."
Undoubtedly, The Witness' piracy popularity is a combination between people being curious because of its critical acclaim, mixed with an unwillingness to pay $40 for an "indie" digital-only title. It isn't ideal, but it's also the inevitable cost of doing business on the Internet. The only way to cut back on it, like Blow says, is to implement some sort of DRM for his next title -- hopefully Blowplay or Blowrigin.