For Airlines to fly over forign countries they have to pay to use their air space.

It said today they are called overflight fees...part of it goes to air traffic control...the rest they pocket....
 how can America control the whole of the Pacific Ocean ......does no one complain...
Do other countries planes fly over North Korea.....does Korea have civilian passenger planes do you know ?

Overflight fees apply to aircraft over flying sovereign air space. The US doesn't own a square foot of ground between Japan and Australia on the most direct route - although some aircraft may just graze US territorial waters around Guam, where overflight fees would apply.
Over the open ocean, aircraft only have to pay for ATC to whom their IFF systems are squawking.

And you're quite wrong about most of what you say. 

First, overflight fees are not just charged for the use of a nation's sovereign airspace, they're charged for the use of airspace that's CONTROLLED by the entity that holds that control. That "control" may be granted by international treaty or agreement or by military action, most likely the former but in the case of your example also the latter. A HUGE chunk of what one would think to be Japanese airspace is still controlled by the USA due to all that WWII unpleasantness and the Japanese loss in that little rhubarb. (Something about them not being permitted to rebuild their Air Force.)

And yes, overflight fees are applicable to over-water flights, depending on who actually controls that airspace. And while air traffic control costs are part of that equation it's not the only part. If you take a look at the FAA link that I posted below you will see that the US controls virtually ALL the "International" airspace over the north Pacific ocean. That WEB site also lists rates for the use thereof.

IFF is a military term (Identify Friend or Foe), not applicable to civilian aircraft. (Ask the Russians and Air Malaysia about that.) But almost all aircraft have "transponders" that are monitored from the ground that "squawk" a four digit code that's assigned to the aircraft for the specific flight. (The system is referred to as RADAR but the ground stations don't really have the ability to "paint" an aircraft and display it to the operator without that transponder getting involved.) All commercial aircraft are subject to using that system and to request a unique code to identify the specific aircraft that can be "dialed in" to the transponder prior to take-off for each flight. Private aircraft in the US are also subject to that requirement with the exception that while flying under VFR Rules a "universal" code may be used. (Transponders are required in almost all operational areas these days, at least in the US.) When the ground station (either TCA or ARSR RADAR) lights up the transponder in the aircraft it responds with that four digit code and other pertinent information such as altitude from the encoding altimeter (hope that the barometric pressure is set properly) and airspeed. Unfortunately even the long-rage system is limited to about 250-miles (earth bulge comes into play at some point) and there aren't many ground stations in the open ocean.

There are additional "unofficial" systems in use that do use satellite communications but they're not required yet, there's no standardization and they're still in their infancy. For example, the engines on most modern jet aircraft stay in touch with "mother" at regular intervals via satellite links that are completely independent of the rest of the aircraft.

Everybody uses IFF, military aircraft in mode II, civilian aircraft in Mode III. In 1988, USS Vincennes mistakenly shot down an Iranian Airbus due to its crew misreading the IFF transponder squawk (correctly identified by the on board AEGIS system) and misidentifying the aircraft as a F14A Tomcat fighter (some of which were sold to Iran under the Shah before the coup) on an attack run, despite the fact that the plane was ascending, not diving as an attacking fighter would do. Captain William C Rogers received the Legion of Merit, he should have been court-martialled and cashiered.

No, . . . there's no dedicated, foolproof "IFF" system in use today, never has been. There certainly wasn't one in use during the "incident" you reference which happened almost 30-years ago. And more than a few things have changed since then. (Nice cut and paste from Wikipedia though even though a fair bit of that info is in error.)

What you're referring to is the standard radar transponder system in use by virtually ALL aircraft these days, not a dedicated IFF system. Military aircraft have dual transponders, or dual function transponders. That's so they can run in controlled airspace with civilian aircraft. They can switch off the civi version and go to the military version only (or both if called for) when they're in "operational" airspace while on missions or during training exercises in airspace controlled by the military.

As to your frivolous demand to court-marshal the Capitan of that ship . . . not a snowball's chance in hades that he should have been. The ship was operating in a "hot" zone in the middle of the Iran-Iraq War. The USS Stark had been struck by a pair of Exocet missiles fired without cause from an Iraqi Falcon 50 a mere year prior so they had every right to be cautious. And there were no operational E3 aircraft in the theater at the time to actually confirm the origin, flightpath, in-flight performance and configuration of the suspect aircraft (the primary reason that the Vincennes with its Aegis Combat System was assigned to the area in the first place; the Aegis System is good, but it's hobbled by being surface-based, no match for the AWACS of the E3.)

Which brings me to your "claim" of an "IFF" System and the error in your thinking. For just a few bucks I can purchase a radar transponder that will "SQUAWK" exactly like that of one on a commercial aircraft. (Check out the avionics section of Trade-A-Plane.) But even worse, the radar transponders on military aircraft can do the same thing as they often operate in civilian airspace. Give that, it's child'splay for a military aircraft to mimic a civilian airliner, especially if the military is that of the same country that originated the commercial flight (they just "ground" the commercial flight at the last minute and send the military bird in its place if they want a clean, unsuspected operation). It's even simple to have the transponder report an ascent while the suspect aircraft is really in an attack dive. That's where the E3 AWACS comes into play as it has a LOT of toys to ID aircraft and what those tracked aircraft are really doing in-flight. So with the lack of that confirmation it was perfectly reasonable for the USS Vincennes to take the action it did. This post was edited by Salt and Red Pepper at September 26, 2017 11:27 PM MDT