How safe are civil flights into Afghanistan?.
Certainly safer than wandering around in Kandahar. Seriously, it's a war zone and as such it should never be considered to be safe to be flying into the country.
The current UK guidelines are:
Air Travel
In May 2009, Safi Airways and in September 2009 Kam Air fulfilled the standards of the International Civil Aviation Organisation (ICAO) and were officially certified to fly within EU airspace.
Ariana Airlines has been refused permission to operate services to the EU because it does not meet international safety standards. Foreign and Commonwealth Office (FCO) employees are not allowed to travel on this airline in or out of Afghanistan.
Some other airlines that operate in and out of Afghanistan may not meet international safety standards.
On 17 May 2010, a Pamir Airways flight from Kunduz to Kabul crashed in the mountainous Shakardara area north of Kabul. The plane appears to have hit a mountain top during some unseasonably poor weather and in poor visibility. All 44 personnel on board were killed, including 3 British nationals.
In February 2005, a Kam Air Boeing 727-200 flying from Herat to Kabul crashed in snowstorms 17 miles out of Kabul. All 96 passengers and eight crew on board were killed in the incident.
In regards to MANPADS, I haven't read the wikileaks documents (due to the server being unavailable) but as I understand it, the threat comes from Stinger missiles (FIM-92's) which we're originally given to the Mujahideen during the Russian occupation, these have a range of about 16'000 feet so shouldn't be a realistic threat to overflights, even if they are firing them from the high-ground. Another point that was told to me was that the Stingers batteries will probably not be reliable after all these years.