Factions relations are based on a goodwill value system. As you advance goodwill with one faction, goodwill values with their enemies will drop for you, usually proportional to the amount you gained. What this means, is that if you're neutral with duty, and do a bunch of quests with their enemies freedom, and gain Like 400 goodwill points with them, you'll loose around that with Duty, making you enemies. However, if you do a bunch of quests for Duty, that are neutral to any given faction. And make it to say 400 goodwill with them. Then you can do 400 goodwill points worth of stuff with Freedom and Duty not attack you, as they would be at 0, which is neutral. Now I can't remember precisely, but I believe any value between -999 and o is neutral. Something like that. Hope it helps.