Board Thread:Theories and Speculation/@comment-26538017-20150629190941/@comment-26545929-20150630065744

Just looked up Black Zetsu's wiki and I quote "Black Zetsu was unaffected, noting that the moonlight could not shine through Sasuke's Susanoo due to his Rinnegan." So everyone inside his Susanoo remained unaffected because of his Rinnegan so it is likely that Nagato would be able to resist the Infinite Tsukuyomi.