The Mojave BoS chapter is easily my least favorite. They claim to want to hoard dangerous technology in order to protect humanity from itself, yet their stubborn isolationism and refusal to cooperate with others makes them an inevitably small faction. Even if the BoS doesn't give a crap about Wastelanders, it would benefit them in the long run to at least be somewhat benevolent with them, which would be easy considering their technology is the most advanced in the entire region. Even the Legion is at least beneficial for caravans, whereas the BoS is hostile to everyone, stealing technology from random people.
Instead of listening to Veronica's common sense advice to expand the Brotherhood's goals, several paladins are willing to murder unarmed doctors all because they're scared of the mere possibility that their secrets about energy weapons and power armor be revealed. By being so hostile to everyone, it's no wonder that the NCR, Legion, and Mr. House all want the Brotherhood destroyed.
All ending slides end with the Brotherhood stealing tech from Wastelanders, or working with the NCR to patrol the highways. The latter is at least a step in the right direction. Working with the NCR, or anyone, instead of fighting them is how you get people to not hate you. If the Brotherhood continue in their ways, they'll just keep making enemies without growing their own numbers. They don't even care for NCR's agricultural technology.
Killing the Brotherhood is the main reason why I feel like siding with the NCR and negotiating a truce is better than siding with Mr. House.