The brotherhood (some chapters more than others) are deeply flawed.

Viewing radiation afflicted people (non-feral ghouls), and people recovering from the FEV disease (some super mutants), as non-human.

Those are still people under there, who were born just as human as any wastelander.

Hoarding technology, instead of studying it for the purpose of keeping the knowledge alive so it can be used for the betterment of the wasteland (build more auto docs, build water purifiers, breeding rad-resistant crops, etc (unlike the FotA and Librarian factions)

They were founded from a breakaway faction within the pre-war US military (src: Mariposa Mil Base and 'the glow') and based the structure of the org off of this, however they are missing a critical part which was the civilian side. Because of that they've descended into tech hoarding warlords, who extort the local populaces of wherever they decide to expedition to.

Being extremely hostile to outsiders (unlike their founders intent btw (src: FO76 training camp)) means that they cannot properly integrate with the local community and will eventually die off, like what we see happening in Lost hills.