When i try to go to Cottonwood Cove the legion attacks me even though my rep displays neutral.

Is Boone still a follower? He will attack them on sight meaning they will attack you too. Even if Boone is waiting somewhere miles away in the waste land, they'll still attack you. You have to tell him you want to part ways.
Also, make sure you're not wearing some other factions armour.

Boone was a "lost follower" at the time. I told Rex to stay at the lucky 38 and all my companions stayed there. I did have the perks from Boone and ED-E though so I'll try an earlier save and tell him to leave. I had no faction gear on at all.
Thanks