Ive heard if you side with minutemen, you will become a brotherhood enemy and need to take down prydwyn. I just finished minutemen's nuclear option, and it made me fail reville, but brotherhood are still friendly.

I can't access airship, but the knights just stand there.

I gunned down a ton of their guys at bunker hill. Don't get it?

The fact that you used the Minutemen to do destroy the Institute probably has something to do with it. Video below (massive ending spoilers) does a pretty good job of explaining.