Not so ironic if you consider that Apple probably has a legal agreement with the NYT company to do so. Just look at how frequently the NYT is featured in Apple commercials and presentations; this doesn't happen just by accident.
The problem here is that the Pulse reader is (from the point of view of the NYT) trying to get a free ride on the NYT's brand name. This is really no different from ripping off any other brand name to advocate your product, e.g., you can't advertise your "high-performance shoe laces" by prominently featuring Nike shoes without obtaining prior approval.