Because Outbrain and Taboola can easily be 1/10th or more of a legit site's revenue, on the order of millions of dollars. I'm not saying that's a good thing, it's a very difficult argument with the amount of money you could potentially miss out on.
It's not a legitimate site any more once it starts making money that way. You might as well sell cigarettes in a health food store. Outbrain and Taboola are cancer and the world would be better off if their offices were flattened by a meteor impact.
The damage to their reputations may cost substantially more in the long run. Doesn't take many "I clicked a NYT article and it was a scam" experiences to permanently sour someone on the outlet.
How many people do care about reputation of a news source beyond "it's mainstream" vs. "it's a tabloid" vs. "it's something random I've never seen before"? I think most people these days don't follow news sites, they click through to individual articles from their IMs and social media feeds.
