Is it safe for a commercial flight to have Iran, Afghanistan and Pakistan on its flight route?

In your particular example, there are a number of international organizations in that area, like the Arab League, the CCASG and the OPEC, which have the UAE as a member. Even if Iran would suddenly start to become as aggresive as North Korea and threaten to shoot down aircraft entering their region, the political and economical repercussions of actually doing so would be extremely severe. They would face embargos, cancellations of trade treaties, heavy sanctions and worldwide punishments. It might even be seen as an act of war, which might start an actual war involving the Arab League.

The threat of an attack from afghanistan is not as likely. Most of the Afghan terrorist weaponry dates back to the Russian invasion of Afghanistan and involves shoulder weaponry with shorter range and outdated launcher platforms. The missiles themselves often don't have an operational range long enough to attack an aircraft flying at 40,000 feet at 900 km/h.

Pakistan's government has been stable for a while and even though diplomatic relations have deteriorated somewhat after the death of Bin Laden, the pakistani government would not take kindly to terrorists taking down a plane from their soil, let alone that they would take one down themselves.

In all cases, any attack originating from the ground of one of those states would have severe international repercussions and can easily lead to political, economical and possibly military action towards that state. Even if it's an action from a splinter group located in that country, it could still lead to military intervention, like happened in Afghanistan after the attacks of 9/11 by Al Qaeda. There are not many splinter groups who would commit such an act of terror with such a prospect.

I have flown into Kabul on a passenger jet, in 2008. The protocol is very simple - the pilot isn't concerned for several reasons:

1. If you are landing, as I was, you are going to be landing at night, because that's when they schedule them.
2. Until they descend below 20,000 feet, you are out of the range of a SAM. Typically, they need to be within 4 miles of their target so at any sort of cruising height, you are safe.
3. In reality, there isn't an easy way to detect what aircraft you are hitting at, and as such, little incentive for taking any random aircraft out.

I say all of this to say - this was for landing in Kabul, and nobody worried. Grant you, when we landed, we had to turn off all lights and close the windows, making us invisible - but if you are just on your way, you are totally safe.

I don't think there's any problem with this at all. Iran and Pakistan are not currently at war with anyone, the security situation is quite safe in both, and commercial airlines service those countries daily.

Afghanistan has been in an effective state of civil war since the departure of US forces, with a weak central government. However, it's unlikely any force would attempt to shoot down a random airliner since there is nothing to be gained and it would be a waste of expensive weaponry. Your main concern is your security on the ground should the aircraft need to make an unscheduled landing due to mechanical issues, but that happens relatively rarely and your aircraft can probably keep flying on to Pakistan or China before setting down.

South Korea hosts a large number of US combatants, but is nevertheless safe to fly over.

Enjoy your trip!

As far as overflying unstable primitive tribal lands like Afghanistan and Pakistan goes, the only worry I'd have is a major mechanical malfunction (not a shoot-down) forcing an airliner to land somewhere in those lands, and being taken hostage. Considering the lack of suitable runways and ATC, it's unlikely that you'd end up surviving the landing anyway. It's more likely that your airliner could glide into a major city with a real airport, where you probably would not be attacked. So, either enjoy your flight, or rebook to a flight that doesn't overfly these areas if you're that nervous about it.

Airliner shootdown incidents are extremely rare. Wikipedia lists a handful per decade and many of those were flights going to/from the warzone and/or flights in propeller planes that fly lower and slower than jets.

For a recognised government there is little reason to shoot down airliners. If they don't want foreign airliners in their airspace then they just need to ask nicely.

Most rebels don't have the ability to shoot down airliners at cruise altitude and the governments they are rebelling against usually have a reasonable idea of what weapons the rebels are likely to have and will set up airspace restrictions accordingly.

Going through Wikipedia removing things that are not jet airliners and removing cases where planes going to/from a country were shot down by local rebels I get.

• 2014: Malasia airlines flight 17 shot down over eastern Ukraine. Apparently a case of the government underestimating what weapons the rebels had available combined with the rebels misidentifying the plane.
• 2001: Siberia Airlines Flight 1812 shot down near Ukraine, apparently in a training exercise gone wrong.
• 1988: Iran Air Flight 655 shot down by the Americans in an apparent case of mistaken identity.
• 1983: Korean Air Lines Flight 007 shot down by the soviets after flying into restricted airspace, apparently caused by a navigation error combined with soviet paranoia about spy flights.
• 1980: Linhas Aéreas de Angola Yakolev Yak-40 shot down while in it's home country following "actions by a foreign aircraft". Apparently accidental, details unclear.
• 1980: Aerolinee Itavia Flight 870 destroyed over italy (possibly shot down by a French jet). Circumstances unclear.
• 1978: Korean Air Lines Flight 902 shot down by the soviets after it violated soviet airspace and was misidentified as an American spy place.
• 1973: Libyan Arab Airlines Flight 114. Got lost, ended up in Israeli controlled territory, was intercepted, refused to land and was shot down.

That is really a pretty small number of incidents and the number seems to be declining, unless you are flying to/from an area with active hostilites or flying over an area with active hostilities in a prop plane I really wouldn't worry.