First some general information. I may not share the actual numbers, but for the sake of calculation we can regard the cost to the airline of the crew, the fuel, and the fees as being substantially identical. This is for long haul international flights, not short ones. Calculating TAROC (Total Airplane Cost of Operation), the overall cost of fuel, the overall cost of crew (including training, pensions, and all other charges), and the overall cost of landing fees, overfly rights, and all other taxes etc, are all exactly the same percentage of overall TAROC or operations costs. Other costs are included in TAROC, like maintenance, cost of money, depreciation, etc, but these are other percentages. This means that fuel economy alone is not the deciding factor, though reducing weight might be. Fees are all based on airplane weight, as are crew salaries, landing fees, fuel burn, etc. Hence the press for lighter airplanes.
Overfly rights are such big business, that some countries, in particular the ‘-stans’ around the black sea, probably earn more from airplanes flying overhead than actually landing in their countries. Ukraine might have been similar; i know Russia reaps a pretty penny from their overfly rights, mainly due to polar routes.
As far as i know, no one ‘tells’, or even can tell, an airline where to fly or not to fly, least of all the United Nations. Its a bit like a Pilot on a boat, pilots advice, but captains orders. Exactly the same on an airplane, controllers advice, captains orders. Now, just like today, cruise ship captains (the only ones I'm familiar with, and then only a little) are subject to all kinds of ‘advice’ from their head office staff, and airplane captains are the same. In other words, the captain files and flies the route previously agreed with his head office staff. All airlines, especially the bigger, international ones, have a staff of meteorologists, and other experts, to advise on possible route structures. These people are also contracted to the US State department, and/or other similar organizations in England, Canada, Germany, France, Israel, Russia, etc, for information on the latest in terrorist or other activity. I don't say they are all associated with the American State Department, or even that they listen, but such services are available, even direct from Boeing.
Basically an airplane files a flight plan just before takeoff, describing the route they intend to take, turning points, heights, etc, though in fact it is legal to change the flight plan in mid flight, more on this later. Per the original flight plan, the airplane PIC (pilot in command, effectively the officer of the watch, representing the captain) notifies each regional controller as he is leaving one region, and entering another. Classically, in this forum, when Malaysia Flt 370 signed off with Indonesia, and failed to sign on with Singapore. The standard language is English, and though heavily accented, and complete with radio interference, usually quite legible. Though technically each controlled region is supposed to get a teleprinter message from the flight plan filing airport, the controllers are quite used to the airplane turning up before the flight plan notification does. Teleprinters are still used partially because it leaves a paper copy at both ends, all date and time stamped. The actual controllers often use the teleprinters actual paper tape slipped into a small aluminum “chip” sliding in a rack on their desk as an indicator of the plane, the chips physical position representing the physical position of the plane.
When very long range operations were introduced, many airplanes could not quite make the full flight with full reserves, so they would ‘file’ for a closer airport, then refile in flight as conditions allowed. For instance, a DC-10/30 could not get from Heathrow (London, UK) to LAX with full reserves, so they filed their flight plan from Heathrow to Las-Vegas. If they struck an unseasonable headwind, then they did have to land in Las Vegas and top up the tanks, missing their connection in LAX. This happened sufficiently infrequently, that airlines accepted this as a risk of doing business. More normally, if the plane experienced little or no wind, or better yet a tailwind, they ‘re-filed’ their flight plan probably somewhere over Canada, to LAX. They could do this ‘re-filing’ because they now had enough reserves to get to LAX from over Canada.
There has been a very real danger for many years from shoulder launched infrared homing anti-aircraft missiles. The Russian “Strella” or SA-7 having been distributed by the millions, and fairly freely available in Middle Eastern bazars. Fortunately they need strange batteries, and an even stranger gas supply, and so far no one has come up with a suitable substitute. Equally, all western equivalents also require specialist batteries, and sometimes gas, so are equally hard to use. I say this because aircraft are very vulnerable during landing and climb-out, and even a rocket grenade (unguided) could do serious damage.
To hit an airplane at 34,000ft requires a bit of technology, and some training, even now. Though a lot of older anti-aircraft missile systems could do this, their radar and fuel/battery requirements are mostly gone now, so making one operational would be very difficult. Equally, successfully launching a newer, i.e. currently operational somewhere, missile requires the coordination of several people, scattered over a fairly wide area, and needs fairly intensive and specialist training as well. Note, the detection radar is rarely the guidance set, and they are usually spaced some miles apart, even if the guidance set and launch apparatus are more or less adjacent. Note; its just too easy to send an air to ground missile down the guidance beam and knock both out.
We have fitted ECM (electronic counter measures) suites, and/or Infrared jammers to quite a few of our commercial airplanes, but i may not share details.