I am playing a new character, although I have already done some Railroad quests, I shouldn't have progressed to the point where the Brotherhood of Steel would out right shoot me for no reason. As I just got to the point where the Prydwin shows up (I just killed Kellogg in Fort Hagen).

So after killing all the raiders in Concord, getting myself a suit of Power Armor and killing the Deathclaw. I noticed some Brotherhood of Steel walking down the street. They didn't do anything at this point, so I went back in to the Museum of Freedom. Story progresses, go outside and... lol wut, the Brotherhood of Steel knights and Scribes are now shooting me. Well at least I got a full set of T-60 II Power Armor to replace the T-45 that came with this frame (and a Gatling Laser to boot). I thought I was in the clear until we came to Sanctuary where another BoS Vertibird started attacking us. Well, true, I guess it would not take kindly to us killing the other Vertibird and all of it's former occupants, but why did the whole thing happen in the first place?

I did not progress through either quest chains far enough for BoS to outright hate me, have I?

Sounds like a bug, the game tells you when you reach a point of no return for faction standing.

Because you are a damned dirty synth

Quite possible, I am playing as a character named Isabel Cruz. Though, I am pretty sure for this Playthrough, I am going to role play that the Mechanist is a Synth, that were created to replace my character when I eventually made my way in to the Institute (I would be the director that would never leave, and the replacement would be my "public face") until the plan went awry and this Synth escaped the Institute, got captured by some Raiders and then became the Mechanist after freeing herself from said Raiders.

But then again, who knows. Maybe The Mechanist is the real Mother of Shaun and the Institute created me to kill and replace her. Which would be really weird if my Character ended up with the Railroad/BoS/Minutemen and causes the downfall of the Institute (right now I am not really sure if I want to stick with the Railroad or become the Director of the Institute again).

(fortunately I am in the spoiler section!)

Anyway, I am pretty sure it was a bug. I think I fixed it by running up to Paladin Danse at the Cambridge Police Station, then running away until it gave me a quest update telling me to talk to Danse. He was non-hostile after the quest updated. And no longer do I get attacked by Vertibirds.

Still would like to know what I did to piss those BoS that were in Concord off though.