Im trying to make a animal companion, The faction it has is the PlayerFaction. If i attack it (By acident or purpose) it starts attacking me instantly. I thought setting it to the player faction stops this? Did i do something wrong or is there some kind of extra option?

You need to set its aggression to 0 or 5 at most. Adding it to the player faction just increases its disposition towards the player. But if its disposition is lower than its aggression, it will attack. Most creatures have an aggression of 100, so they will always attack.

Same applies to NPC's too, btw.

Doh, Didnt notice that. My bad, Thanks very much.

One more thing, Whats the difference between setting it to 5 or 0?

Have a look at the definition of aggression http://cs.elderscrolls.com/index.php/AI_Button. Basically 5 means it will defend itself. 0 means it won't even do that.