NYT is a premium venue for people who want to advertise, because its regular readers (especially the ones who don't live in New York) tend to have above-average disposable income. Because of that, the NYT should be able to charge a premium for advertising with them.
But if they opt into the ad exchanges, then they've given ad exchanges a signal they can use to more easily track who is a regular NYT reader. Advertisers could use that to target NYT readers without ever actually advertising on the NYT's website - they can follow them somewhere cheaper, and advertise there instead.