As has been bitched about alot on these pages, your reputation with the various factions is fixed by the storyline and whatever harm/good you to to your reputations is pretty much erased by the completion of any mission.
In MP or after you've finished the storyline you'll have total control over who will speak to you and who wont but until then you are like a bretonian poodle to its liberty master...

yep they dont like you much in the beginning, you can check your rep rating for them during the missions, and normally people wont talk to you unless you are either completely neutral or friendly

Yup. Your reputation with them just starts with 3 bars in the red. Still Neutral, but on the wrong side. (if you want them to be your friend that is)

Just kill a couple of their enemies and they'll clear up.
I could already talk to them after my first mission. I didn't go back to Juni and just went on killing some more annoying pirates.