First playthrough, I’m locked into house ending but now have to kill BoS. Why quests will make me hate them?

I was between house and NCR and then NCR told me to kill house so I went with his questline. Blocked me off NCR main quest and I killed all of Caesar’s camp with Boone. I knew I’d have to kill BoS but after they >!strapped a bomb to my neck and made me do their bidding!< I wasn’t too upset with it. But after doing their main quest I’ve become less okay with killing EVERYONE who’s BoS. Followers of the apocalypse are my favorite faction (though I haven’t been able to do any of their quests) but apparently there’s some quests that show the BoS acting poorly towards them? In general my character is fine with ridding the wasteland of those who kill over ideology so any quests that make BoS seem bad would’ be welcomed, thought I’d ask here instead of spoiling myself on the wiki