Bike Jihad and troubles on the road...
If the first casualty of any sort of political and social unrest is truth, the second caualty is tourism. The tourists, including cyclists, simply disappear.
Team Pumpy rode Nepal at the height of the Maoist unrest - July '04 - and not once encountered a problem. In fact, one of the good things about the ride was that Kathmandu, usually jammed to the rafters in July with backpackers, was almost devoid of tourists. Now, whilst this isn't good for the local economy, it does have its upside for the more individually minded cyclists amongst us.
As far as extremist Islam is concerned, Team Pumpy didn't see a bomb, an Islamic protest, nor even a burqa (the full-faced garb of choice of the more strict female Muslims) on the whole trip.
There are trouble spots in the world worth avoiding, but it simply keeps needing to be said that the media, by its nature, distorts our perception of reality. You really do need to read between and beyond the sound bites and video grabs to get any kind of 360 degree vision.
The fact is that 99.9% of people you meet on the road are normal folk, no matter their religious beliefs or political affiliation, and they will treat you with respect. The other fact is that, on a purely empirical basis, your chances of getting blown up anywhere are extremely slim if you think about things on the time-space cycling continuum.
Things always look bad on the tube, and your own fear may be the biggest hurdle.
The best thing to do when plannning a ride, and in some doubt as to the safety factor, is to go on the internet and talk to experienced cyclists who have been whereever it is you plan to go. And believe me, wherever it is you are going, somebody has already been there, on a bike.
For my money, you cannot beat international cyclists' first-hand experience as the prime source of your 'safety' information.