1. How do the counter measures work? They fly forward, away from the missle and the missles always hit me. Do I need to face the missle for the flares to work?
Most missile shots in the game are face shots (the target shoots at you while you fly towards him.) The normal method of use works like this: pop flare, cut onto a new divergent angle, kill the augmentor (afterburner). If you don't kill the AB, the missile won't lose lock because your engine's signature won't get small enough for the flare to attract the missiles attention. No, you don't need to face the missile, just change direction, fast.
2. Why do I usually only have 1 wingman? We are supposed to patrol the sector with just 2 of us? I'm always getting up shot because once I survive the first fight, there are more enemies at the next waypoint.
This is a function of how these missions are scripted. Normal patrol missions are 2 fighters. The random part is how many baddies you will meet. 4-ship missions are normally reserved for anti-ship and ground strike. Once you become a carrier commander, you can change this, of course.
3. When I'm flying trough the air at a planet, the only way I can turn is by banking the ship. Is that normal? If I use the rudder, I think it's a rudder, I just look in the direction I want to go but the ship is still flying in the old direction.
Yes, this is normal. In the real world, hitting the rudder at high speeds tends to result in sometimes unrecoverable spins and many modern fighters have flight control software that locks out the rudder above certain speeds.
Hope this helps.