I think this is a bit of an oversimplification. Most people have a perception bias for "bad" people, but it's justified because the potential outcomes of being a victim of a bad person are astronomical. So it doesn't matter if the vast majority of people are "good", because a single encounter with a bad person can be catastrophic, so it makes logical sense to be wary if you know there are any amount of bad people around.
Now of course this instinct gets manipulated by the media and politicians and all that, but the initial instinct is perfectly reasonable, imo.
These are valid points. Cooperative groups outcompete non-cooperative groups and humans have evolved around that. But that aspect of human nature evolved in a radically different context to the modern world. Cooperation evolved when humans lived in small groups at the scale where everyone knew each other and "bad" actions were always known about by everyone in the group and usually punished/discouraged in some way. People outside that group were always viewed with suspicion and wariness. The human brain is hardwired to identify and categorise everyone into "us" or "them" groups.
When human groups grew to the size where it was normal to interact with strangers then that radically changed the way that human cooperation had to work, the rules are very different than the ones we originally evolved with. As you said, organised religion and governance specifically grew out of the need to manage this. In a large society with ubiquitous anonymity, it is much more feasible to be non-cooperative and still be successful in an evolutionary sense (i.e. have plenty of surviving offspring). Modern human societies, with specialisation of labour and market economies, enable this and I think can be argued even encourage "bad"/non-cooperative behaviour in many ways.
I completely agree. But it's difficult, because forming trust with a bunch of strangers goes against human nature. You need to find a way to get people's brains to identify those strangers as an "us" instead of a "them".