Using the RSS feed bypasses the ads.Now that I think of it, what a stupid reason for The New York Times Company to complain about this.
They were essentially complaining (on behalf of The Boston Globe, Boston.com and The New York Times) about the fact that Pulse pre-loaded their RSS feeds and used them in an unauthorized, commercial way. I suppose that the app featuring The New York Times may help Pulse sell the app (and so would the NYT's positive piece about Pulse). Having the NYT RSS feed in Pulse isn't anything that any user couldn't add in regardless. So the end result here will be that Pulse will remove these RSS feeds from being pre-loaded from Pulse ... which will likely result in less people seeing The New York Times and Boston Globe's content. What is the point of The New York Times Company doing this? They are just preventing their content from being prominently featured.
There's a difference between pre-seed an RSS feed and allowing users to enter the RSS URL manually after install.