You're correct of course, but I don't really see how this isn't a vacuous observation. Yes clearly our perceptions are at odds, but that has nothing to do with the reality of whether or not they
need to be doing that tracking. Obviously they think they need to, or they wouldn't do it. But I think I've laid out a pretty strong argument that they actually
don't need to, which leads me to believe that they actually haven't considered it seriously enough to give it a shot.
Would they be as profitable? Maybe, maybe not. Would they become unprofitable? No, strictly speaking. I'm confident in that because the NYT weathered the decline of traditional news media before the rise or hyper-targeted ads, and because I've maintained a free website in the Alexa top 100,000 on my own, with well over 500,000 unique visitors per day. That doesn't come close to the online audience of a major newspaper, but it's illustrative. There is a phenomenal amount of advertising optimization you can do using basic analytics based on page requests and basic demographic data that still respects privacy and doesn't track individual users. I outlined a few methods, such as Daring Fireball's.
Maybe instead of this being a philosophical issue of perspective between a user and an organization, it's an issue of an organization that hasn't examined how else it can exist. Does the NYT need over 10,000 employees? Is there a long tail of unpopular and generally underperforming content that nevertheless sticks around, sucking up money and forcing ever more privacy-invasive targeting? If the NYT doesn't know its audience well enough to present demographic-targeted ads on particular articles and sections, what the hell is it doing tracking users individually? It's just taking the easy way out and giving advertising partners the enhanced tracking they want. But they don't need to do that, and whether or not they think they need to do it is orthogonal to the problem itself.