Not sure how to fix it, I haven't attacked any of them, I've not done any missions which should have directly conflicted with them for other factions. I've literally just done the mission where you

Spoilers

Kill the Institute Courser, and I've fast travelled back to the hideout and everyone wants to kill me.

Not sure how to fix this.

Have you tried sleeping for a full 24 hours? Some say that helps.

Thanks, that seems to have done the trick!