the new PvP protection system works like this: if you have good morale (-30 or more) and did not just run away from PvP by logging out, you will get a window pop up each time your log in you character.
This pop up asks if you wish to activate PvP Protection. If you click "accept" you will be permanently green name for this session (aka, until you log out your character). If you click "cancel" you will be white named for the session, which will allow you to participate in PvP.
Remember that some monsters and events require you to be "flagged" for PvP, which means you should not activate PvP Protection if you plan on doing these.
I hope this helps clear things up.