His reasons were:
1. Floyd was old and had been inactive prior to the fight, so that had to have its effects.
2. Floyd has always been a patient counterpuncher.
3. Conor fought on the outside and used his length.
Atlas had McGregor winning the fight in the early going but thought it was obvious that he was winning the battle while losing the war. At a certain point Floyd changed up his style to something he doesn't usually do and went after McGregor and ended the fight. He's not saying Floyd was in real danger of losing so much as that he doesn't think Floyd purposely lost rounds or slowed the fight down at all to carry McGregor.
Atlas never calls McGregor a good fighter. He carefully dances around it, but he does say McGregor's strategy in the fight was smart and that his promoting was brilliant. He does emphasize that MMA fighters will never look good under boxing rules because they aren't as dangerous without all the weapons they normally use.
Finally, he notes that Pacquiao and McGregor have the same manager, so he thinks the fight will get made. Pacquiao is also older, etc, but he says he thinks Pac will end him earlier, because his style is more aggressive.