How do I go to The Fort from Cottonwood Cove if I'm vilified by the Legion?
Solution 1:
You can still us the raft that Lucullus would offer you. Approach the raft and press the interact button to travel to The Fort.
If you’ve already been to The Fort then you can fast travel there.
You can do this even if you are vilified by the legion, but you’ll be shot at once you arrive. You can wear legion armor as a disguise, but the many guards at The Fort will quickly see through it.
If you were already willing to kill everyone at Cottonwood Cove then I wouldn’t expect there to be a problem with killing everyone in The Fort
Solution 2:
If you already had the Mark of Caesar before you got vilified by the Legion (from Fallout Wiki's "Render Unto Caesar" article):
If you become vilified by the Legion at any point during this quest, it will fail and the free quest Beware the Wrath of Caesar! will start.
You won't be able to continue with the main questline for the Legion if this is the case.
At this point, there are two options to get to Benny at The Fort, but both of them will require fighting or killing. From Fallout Wiki's "The House Always Wins II" article:
(The article describes how to get to the bunker in the camp, and not to Benny, who is in Caesar's tent. Most of it should still apply, though.)
If you've once again become vilified with the Legion, or simply don't like the Legion, you can still complete this quest.
The first option is to disguise yourself as one of the Legion. Don't take your companions as the guards will notice and a shootout will ensue. Make your way through Cottonwood Cove to the Fort as normal. Speak to no one but the dock officer and avoid all legion dogs or else you'll be caught. Make your way to the bunker. The guards inside will recognize you, but they can be killed without alerting the rest of the camp as long as you remain disguised. Complete the mission as before and return the way you came.
The second option is to simply kill everything in sight. Instead of speaking to Cursor Lucullus, whom you'll have killed, just target and activate the raft to get to the fort. Kill everything between you and the bunker and complete the quest as normal. You don't have to kill Caesar if you don't want to.