El Al (and other Israeli) aircraft are equipped with infra-red countermeasures since fire at Arkira B757 in Mombasa in 2002. Infra-red counter-measures are relatively simple (it has a small radar to detect missiles and if one is detected, dispenses burning decoys), so it can be mounted on almost any aircraft. The system however poses additional fire risk (the flares have to burn very hot and the system has to be able to ignite them), so it is only used in areas where risk of terrorist attack is high. Switzerland (and possibly other countries) even prohibit it on their territory. Apparently laser-based system is in development to resolve the fire issue, but it will still only work against IR-guided missiles.
But for radar guided missiles like the Buk system probably involved in this incident there only seem to be three defences:
Hit the tracking radar with your own missile (like AGM-88 HARM) before they hit you. Fighter aircraft is obviously needed to carry it, though most fighter types could be used as they only need radar detector and suitable hardpoints.
Generate sufficiently intense microwave signal that it overdrives the detector in the missile head and effectively blinds it. This is heavy, expensive and requires power (not outside the range of common aircraft generators, but the increased fuel burn would probably be noticeable), so even most fighters don't have it. Instead the system (like AN/ALQ-99) is mounted on special-purpose aircraft like EF-111A Raven that gets included in attack group trying to penetrate enemy territory with heavy air defences.
Minimizing radar cross-section, ie. stealth. That requires completely different designs that are aerodynamically less efficient, because the funny shapes are necessary part of being stealth and that are not trackable by ATC surveillance radars.
Obviously the first is out of question for airliners - carrying any weapons or munitions of war on civil airliners is prohibited by Convention of International Civil Aviation article 35.
While the second would be technically possible (E-4B, an airborne command centre, and VC-25, the Air Force One, are modified Boeing 747s and both have counter-measures against both IR-guided and radar-guided missiles), those modifications would be a heavy, expensive and complex protection against something that has only happened a few times.
And the third would have too many disadvantages. It would hide the aircraft from ATC surveillance radars that have averted many more accidents than were caused by missiles and it would require new, less efficient designs that would be massively expensive. Just few month ago we wanted MH-370 to be seen by radars. We can't have both.
Staying away from the war zones is a safer option anyway and is normally possible. In this case likely explanation why MH-17 didn't is that the Ukrainian authorities were not aware that the rebels have this air defence system, assumed they only have a lighter-weight one (those are often usable to about 20000'; the military aircraft shot down on previous days were lower) and only closed the airspace up to FL320 rather than completely.