I'm comfortable there is certainty. There is considerable evidence that the passengers attacked the hijackers, from multiple different sources including mobile calls from passengers to family, air traffic control and the plane's black box. Each one of these lines of evidence involved at least dozens of people who would know there was a cover up, maybe hundreds. None of the people involved in accumulating that evidence have any vested interest in supporting a cover story. So the cover up would have to encompass civilian, government and military personnel, employees of multiple companies and victim family members. That's way too many for me to accept as remotely reasonable, especially when much of the evidence came out very quickly, before any possible cover up operation could have come into play.
As with any of these conspiracy theories, it's useful to consider who would know about the cover up, who would have to be actively involved in promoting it, and what their motivation would be. Take the flat earth as an example. There are tens of thousands of aircraft in the air at any given moment, all of them navigating using systems that assume the earth is a globe. Before modern systems, pilots and navigators calculated routes by hand. They all assumed the earth is a globe and if they were wrong their calculations would all have been massively in error. So essentially every single aviator in all of history and every nation on Earth would have to be in on the conspiracy. I've not even started on marine navigation.
If the plane had been blown up by a bomb or shot down, it would have broken up into chunks which would have landed largely intact, because fuselage sections are quite light compared to their volume. You can see this in pictures of other downed or bombed planes, such as the one shot down over Ukraine. Most of the bodies would have fallen out of the plane or come down in the fuselage sections and been mostly intact. Bombs and missiles simply don't destroy the whole vehicle so completely.
The only way the bodies could all have been so thoroughly destroyed is if the plane smashed into the ground as a single piece under power at full speed, which would require full control authority for the pilot. Even if it had drifted or spun into the ground, perhaps due to loss of control from a small bomb or weapon damage, it would have been too slow for the observed effect, because we know what those crashes look like as well. The speculative electronic interference weapons would also have induced a more conventional crash, not one at full speed under power.
Also the article even opens with an eye witness account of the intact plane hitting the ground under power, the witness even describes the engine noise.
It is possible a small bomb or grenade did go off, but wasn't powerful enough to disable the plane. However if it did happen that just supports or at least is consistent with the passenger revolt theory.
What the article tries to do is throw out as much information presented in as discordant a way as possible, to create openings for speculation. However the conspiracy scenarios presented don't actually fit the evidence at all. all the rest about mysterious planes and such is irrelevant noise to the facts of the crash itself.
As with any of these conspiracy theories, it's useful to consider who would know about the cover up, who would have to be actively involved in promoting it, and what their motivation would be. Take the flat earth as an example. There are tens of thousands of aircraft in the air at any given moment, all of them navigating using systems that assume the earth is a globe. Before modern systems, pilots and navigators calculated routes by hand. They all assumed the earth is a globe and if they were wrong their calculations would all have been massively in error. So essentially every single aviator in all of history and every nation on Earth would have to be in on the conspiracy. I've not even started on marine navigation.