But what if he doesn't know he's in a Genjutsu?Well after my knowledge and my believes about the Rinnegan then it's impossible to disturb the host of Rinnegan with Eye Genjutsu.
Reason why is: Since we all know by looking on Nagato that he learned high level jutsus in every element in a very young age, and we do know by sensing chakra they can find out by using a special paper to see what element they are. So, by learning and perfecting two different elements like Jonins.
Still it has something to do with Chakra control by mastering all the different elements (in my beliefs) So because of Nagato mastered all these elements at a young age it would mean that he have a perfect chakra control, and all who had Rinnegan seems being enabled to use the six paths and as well all the elements.
And I believe Perfect Chakra control > Tsukuyomi.
Perhaps this didn't make lot of sense.
Summary : Host of Rinnegan gains perfect chakra control, and perfect chakra control > Tsukuyomi.
And Genjutsu isn't the only thing Nagato should watch out for
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