This isn't an endorsement, if anything it's just positive coverage of this agreement. Take your EFF fear-mongering back to when this was posted yesterday.
As the article mentions, it's very likely that New York Times hasn't seen the agreement. Otherwise they could just leak it to the public. So what do they endorse?
However one might feel about IP enforcement, reducing tariffs and aligning similar but slightly different regulations can help economic growth in all the nations.