I have the quest to go kill or disable Mr. House which requires a trip to Cottonwood Cove, however when I get there everyone is hostile and attacks on sight. What quests are there to increase my legion rep?

If they are attacking you on sight, I don't think reputation has anything to do with it. Did you kill anybody important? Are you wearing NCR armor? Is Boone in your party?

Maybe try wearing a Legion armor.

Yeah Boone is in my party. I have to get rid of him then?

Yeah, Boone is always hostile to the Legion. So going to Cottonwood Cove/The Fort with Boone is always a bad idea if you want the Legion to stay on your good side.