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Since nearly everyone who is mad seems to have their own unique reasons or flavor of reason, I think that there's more likely to be a single, more elusive cause that hasn't found expression yet. The alternative would be that she did a dozen things wrong, which is unlikely. She did one thing wrong, and it's finding different expressions in different people as they try to understand their negative emotions. That's certainly the case for me. The friend thing is just the tip of the iceberg, it's the entire monologue that is at issue.
Fauna, as an atheist, materialist/nihilist doesn't really understand that it isn't all about her. Aside from being parasocial with Fauna herself, saplings could also be social with each other and come together with her in a kind of collective performance. There is a spiritual aspect there of a group of people who have chosen to hold up a belief in something they themselves know to be absurd. They do it for the same reason everyone else does similar things in the context of religions or other causes, because it gives them temporary relief from the drudgery and pain of the material world.
What she did that is making people angry on a fundamental level was to rip the heart out of the performance, rendering it just another empty transaction in a world that is too full of those already. That's depressing and tiresome and not a little condescending, but it was inevitable and flows honestly from her most deeply held materialist beliefs. I also wonder if that's why JP has it so much easier avoiding these things, because they still have the blood of pagans running through them and can understand how people might find some solace, meaning, or community in the harmless worship of minor gods.
To put it shortly: just because Fauna was correct doesn't mean she's right. She's correct in what she said, in a material sense. What baffles so many of the tourists and has since the beginning is that she might also have been wrong.