I'm doing the wildcard quest that asks you to make contact with all the factions and FINALLY found where I'm meant to see the BoS but as I go to the area (Hidden Valley) three patrol units appear and attack me immedietely. I'm positively aligned with the Khans and neutral with everyone else as far as I'm aware. Does this mean I can't make contact with them if they're just going to shoot me on sight?

This happened to me too, it was because i was wearing an NCR outfit. Try wearing an outfit that isn't part of a faction.

I was wearing reinforced leather armor and changed it to the Vault 21 suit and still got attacked?

Anyone?

You didn't tell the NCR ranger in the bunker about the BOS and they're still attacking?

Are the BoS and Khan enemies?

No, and did you appear at the bunker at night? If so then I believe they will attack you. If you killed any of their scouts before hand then they will also attack you...

You can kill all the BoS and still move on with the quest, but it is very hard though.