Jonah highly HIGHLY distrusts and hates humans-- but between him and Jones he is the FAR more reasonable one.

Jonah hates humans for a multitude of reasons and had personal experience himself. One of the major ones was he was shot by the celestial (Mjosgard) that snatched Siegel, as he was with him at the time, because quote "I don't need another great white."

His opinion on just everyday humans though is VASTLY overshadowed by the hatred he holds for the FMI monarchy and for celestials in particular. So while he doesn't like humans he thinks there's a deeper issue than just randos. The people in charge make the laws, they set the ground work-- THEY'RE the ones that legally classify them a certain way and it trickles downwards. Want to be treated equal? Get rid of the ones in charge and work from there.

Over time his opinion doesn't REALLY change all too much-- there is nothing that could make him fully trust humans-- his experiences are just too engrained. But he focuses elsewhere and doesn't bother humans on purpose-- only if they bother HIM.