It wasn't the message on Obama, which I've not heard any Republican - even establishment - criticize that. Rubio was his own undoing.
They NY Times will magnify any inter-Republican spats and we all know that Christie was attacking Rubio over his repeated comments about Obama’s actions being fully planned and purposeful.
This article didn’t have any obvious thesis, except that Rubio failed because of his spat with Christie and “he was sweating a lot.”
I simply wouldn’t give NY Times any credence in an argument why you don’t like Rubio. There are certainly more valid reasons than anything the NY Times has to say.