In regards to Neelix, I also sort of often got the impression that he knew the crew found his antics laughable, but that it didn't bother him because, in a sort of innocent but ethnocentric way, he considered himself the superior life form. Not that he felt anything bad towards humans or thought they were stupid per se, just...for example, I love my dog to pieces and consider him to be super smart for a dog but would be more inclined to be amused than offended if he thought I was the cute, funny one.
Yeah that! Though for me, it was not so much that he was superior as he was he seemed to find them a pessimistic bunch who went in search of trouble. He even got pissed at Janeway a few times for it whether it was examining a nebula or strange phenomena. I remember a few episodes where he thought she was craaaazy for peeking into every nook and cranny they came across. Looking back, I suspect he thought they were all a little nuts.