Right now, the greatest threat to airliners from missiles are the small, shoulder-mounted SAMs that have proliferated far beyond their intended users. These MANPADS (man-portable air-defense systems) can be employed to deliver a heat-seeking missile from a couple miles away and a few thousand feet below. To defend against a heat-seeking missile, one needs to convince its seeker head to lock onto something other than the hot engine on your aircraft. This can either be something a littler hotter nearby that masks the engine signature, or something hotter all over that masks everything. Since flares burn out and fall away, the second option may be the winner.
Enter Skyshield, an aircraft-mounted laser that can detect the heat from a fired missile and train its energy onto the sensor, blinding it and likely sending the missile away from the intended target. Unfortunately, like everything else, it costs money for the acquisition, aircraft modification, and maintenance.
It’s also useless against radar-guided missiles. The good news—until Malaysia Airlines Flight 17, at least—is that these systems are generally held by more responsible parties and less likely to get into the wrong hands.
Another option for in-close protection might be an airport based system like Skyguard. This has towers with heat sensors and lasers which would do the same thing as the Skyshield, but would only be required to be built at questionable airports.
The problem with flares and chaff is that modern systems easily look past them as they fall away, seeking the originally-tracked object. Dispensed countermeasures are mainly useless against modern systems unless accompanied by serious maneuvering, something airliners are unable to do.