The limitations of radar are part of the reason why Aircraft have transponders - you can pick up an actively broadcasting radio from far greater range, and you're not relying on getting a clean bounce back from the aircraft. They're also the reason why carriers carry multiple E2s - a radar on the top of a mast on a ship simply can't see far enough.
Every countries spend literary billions to develop radars, stealth fighters and ways to disrupts radars. Now, we understand in a closed area watched by several nations and operating by clear weather, they can't effectively localise one big civilian aircraft? For 4 hours? Because just the guy turn off transponder?
I think either we have been seriously mislead of what our technologies capabilities are or one of states of the area in knowing more than it said.
Moving to ground radar, many counties simply don't have total coverage. When a transponder works fine the vast majority of the time, and peacetime is the prevailing norm, there isn't a cost justification for it. The prices involved in covering fast stretches of ocean and remote islands with radar coverage is a hard sell.
Just from reading comments in the linked piece, it seems that is true for some parts of the world. The malay military didn't have an operational air defence radar system, or they might have had a better idea where it was going. And there are areas around the Bay of Bengal with no radar coverage either, which, if the plane was hijacked, might be where it headed.
On 9-11, the combined maximal efforts of civilian and military aviation were unable to locate four airliners because their transponders were turned off. This occurred near the New York and DC metropolitan areas, some of the most carefully controlled air space in the world.
Without a transponder, an aircraft is just a raw radar return among, potentially, hundreds or thousands of other returns from civilian and military aircraft, weather, birds, balloons etc. Add to that glitches, ghosts and anomalies in busy air space and it is not surprising that a large aircraft without a transponder can hide in plain sight.
Primary radar is difficult and inconvenient but it's not nearly as difficult as you make it sound.
Andrews scrambled two (unarmed) F-16s to intercept flight 93; they just followed the Potomac north because no one knew where that plane was. Even after the PA crash was confirmed, those fighters spent hours contacting radar returns to check them out and get them to land.
1. The plane exploded or immediately crashed roughly where the last known contact was made. No debris has been found because... well, that's a weird one.
2. The refuted claim that Malaysian military radar tracked it to the Strait of Malacca is actually correct, and it crashed over there somewhere.
3. The plane continued flying but stayed over the open ocean, far enough from land that there was no primary radar coverage, and eventually crashed into the ocean somewhere far away. There isn't a whole lot of room for that in this area, of course.
4. The plane eventually flew over land but the local air defense people were asleep at the switch. It subsequently landed or crashed in that country or in the ocean beyond.
5. The plane eventually flew over land and was tracked by primary radar but this is being covered up, either to hide incompetence, or as part of some crazy plan where the plane was hijacked and stolen by that country.
IMO anything beyond #3 on this list is seriously far-fetched and not a realistic possibility, but I wouldn't rule them out completely at the moment.
Just 10 years ago someone has stolen a Boeing 727 from an airport,took off, turned off the transponder and landed somewhere. Even FBI looked for that plane and couldn't find it. So I guess it's very much possible to fly undetected.