The simple answer is that not all poisons are lethal; the fact that Lusamine survived is evidence enough that Nihilego's neurotoxin is, in some circumstances at the very least, not lethal. Something else to take into account here is dosage. The amount of Red Bull Fizz ingested on his last bender wasn't enough to kill him, but if you let an ant drink the half of what he had, it'd probably die, and likewise too much of something that isn't inherently poisonous, for example, drugs of any kind, can be poison in excessive doses, because every rose has its thorn.
There's more about Nihilego's that suggests why it shouldn't be deadly to its host. Its Ultra Beast name, Symbiont, suggests that, rather than just being a parasite, there is a sort of mutual benefit. Also, as per Bulbapedia:
When Nihilego latches on to a host's head, it does not manipulate its actions directly. Instead it awakens the host's own capabilities and boosts them to an extreme extent in order to protect itself.
I don't know about you, but I don't think it'd be beneficial for an organism that uses its hosts to protect itself would benefit from having lethal neurotoxin.
"When I said 'deadly' neurotoxin, the 'deadly' was in massive sarcasm quotes. I could take a bath in the stuff. Put it on cereal. Rub it right into my eyes. Honestly, it's not deadly at all. To me. You, on the other hand, are going to find its deadliness a lot less funny."
