Well so far few things come to mind.

First the hints the game gives you as to the Hunters connection with the state Yharnam is in. One NPC keeps berating you and actively hates you for being a hunter as she thinks this is all the Hunters fault. Maybe there's a connection between the two. Maybe the hunters did bring this situation on Yharnam. As a side note the game also makes it very clear that Yharnam was a solitary state with an active hate to outsiders.

Another thing that come to I found interesting is as soon as you go into Old Yharnam you hear a voice asking you to leave as the beasts here pose no threat to anyone from above. This made me think of I am legend, the book, and how that maybe the beasts there have reached some sort of civilized existence and this whole thing could be a "natural" evolution of mankind.

The game's central theme is Lycanthropy. Throughout the various cultures, lycanthropy is often associated with a curse or a infection brought on by the misdeeds of a person carrying it, though many times it is infection by proxy. Could it be that maybe the stat that Yharnam is in is because they are being punished for something they did?

As far as the Healing Church. I think they have a pretty strong connection to the beasts. I think they experimented with blood magic and somehow infected the whole population.

Also, Notice that other Hunters you meet in the game has their eyes covered. Could it be that the Hunters are punishing themselves, or being punished, for something they did or didn't...

I would love to hear some of your thoughts

UPDATE: So all the bosses seem to be former hunters that somehow parted ways with their respective lodge which makes my theory that the hunters and the healing church are responsible for all of this.