Excuse my ignorance but what can these military planes do to protect the passengers??
I disagree galaxy flyer!
While its clear that QRA jets will not be able to save the passengers on board a hijacked aircraft, if the hijackers have full control of the flight deck and are intending to crash the aircraft, there are other benefits of having a military aircraft near by.
For the passengers and crew specifically it will provide the comfort of knowing that they are not alone and that someone is aware of their situation and working a solution.
For everybody else (ATC, other aircraft in the vicinity, decision makers) there is the benefits of knowing the hijacked aircraft exact location, speed, heading, altitude and other relevant information that an observant military pilot can provide (number of people in the cockpit, movement in the cabin etc.). Remember that it only requires the transponder to be turned off, for all the civies to lose track of the aircraft (ATC is blind, TCAS does not provide warnings - primary radars (if available) are not precise enough to provide propper seperation to other traffic).
For the people in the probable target building (9-11 scenario) it might be their rescue, if in a country where leadership are willing to make that extreme difficult decision and order the aircraft downed before it reaches its intended target.
Last but not least it will affect the hijackers. They now know that somebody is there to intervene with their plan, and that they might not achieve their objective.
My point was more about the geography... Except for France, Spain, Germany and maybe Italy the timing from contact lost, intercept and action is just on the edge of the impossible. Case in point a few years ago (Feb 2014) the Swiss air force was scolded for not being able to intercept an Ethiopian Airlines aircraft that was hijacked by an apparently mentally unstable pilot (!) to Geneva. Problem is that the plane was only for a few minutes in Swiss airspace, escorted initially by Italian then French fighters. What was the chain of command in this case ?!
Regarding atakacs question above, I think the reason for the Swiss not being able to react, has more to do with them being a neutral country working on their own. All other NATO countries are interconnected (chain of command wise) when it comes to the protection of their airspace. This means that if an aircraft is intercepted over Germany and the situation is not solved before it enters for instance UK airspace, UK QRA jets will be ready to take over the intercept when the aircraft crosses the FIR boundary.
I have personally been on QRA missions where the target aircraft was followed by QRA jets from 4 different countries during its flight, with each QRA handing it over to the next QRA at the FIR boundary.