I know I can kill synth patrols without the institute getting mad but can I shoot down a vertibird or massacre the random brotherhood patrols without upsetting the rest of the brotherhood?

Yes. I've downed several. One was hostile when I first saw it, but the brotherhood is still not hostile.

I know you can safely shoot down the vertibird, but I thought if you shoot up a patrol the BoS becomes hostile.

As long as you don't kill any named character, you're OK. If you do kill a named character, all bets are off.

thanks guys