Did you listen to what the guy from the FBI, who had conducted a related study, had to say?
Yes. It was hard to find the objectiveness around the Daily Show snark (they clearly are trying to push a position, it's not like this is an objective report). However, in his 3% number, he's merging ALL shooter events and saying 3% of the time a good guy with a gun stopped the attack. How many times was there no one with a gun around but the bad guy? Additionally, even if it were 3%, that would still be 3% better chance than with a gun.
As for the examples where the reporter tried to respond to a live shooter, that "simulation" was hilariously inaccurate, and the reporter clearly wanted nothing to do with a firearm. His "dancing away" during one of the encounters shows he wasn't serious.
Again, it was an entertaining watch. But much less factual than it was probably perceived by you to be. I practice rigorously with firearms, and I know better.
Additionally, multiple law enforcement agency heads have come out recently urging citizens to carry a weapon. They seem to be at odds with the guy from ALERT in this video.