I think Jon has the same fatal flaw that a lot of liberals and progressives do, in that he believes most everyone is good hearted, and when they do bad things, it's because they're misguided. Some folks seem to think that all that's necessary is that we sit down and talk in good faith and respect, and offer people correct information and compassion and they'll come around. (This is, of course, similar to the well-meaning libertarian fallacy that if we just stopped trying to control people, they'd behave sensibly on their own.)
Undoubtedly, most people mean well. They're doing the best they can with their experiences and knowledge to make the best life for themselves and their loved ones, and when they do harmful things, it's because either they don't know any better or they have a disproportionate sense of fear about doing things differently. There are a lot of people who are doing very bad things who nonetheless have larger goals in mind that they believe justify the means. (And in some cases, that is true.)
But those aren't the only humans on the planet.
We're into facts and information, of course, so here are some: Some people are sociopaths. Some people have something actually wrong with their brains that makes it impossible for them to empathize the needs and feelings of others when acting. Most sociopaths are born that way, some are created (early childhood trauma can rewire neural pathways in scary ways) but the common thread is that they cannot be changed, only controlled.
Unfortunately, sociopaths often get themselves into positions of power, including political power, and that's where the whole hand-holding, Kumbaya-singing idealist vision of a progressive Utopia falls apart.
To put this in terms that Stewart would undoubtedly understand, let's look at the classic alignment grid:
In this grid, Robin Hood would be considered chaotic good, Darth Vader would be lawful evil, Jack Sparrow, chaotic neutral, etc. (Jon himself, as with most other court jesters, would probably be a chaotic neutral as well. Maybe chaotic good.)
It's sometimes said that even villains don't think they're villains, but that's not quite accurate. Some villains know very well that they're the bad guy, and either don't care, because their joy matters more than someone else's pain, or actively enjoy watching others suffer.
In these terms, Jon's fatal flaw is that he thinks Bush and others like him are aligned in lawful evil: People who believe they're doing the right thing when they harm others. I don't think that's the case. I think many rank-and-file right-wingers are, but GOP and Tea Party leadership generally falls into either neutral evil or chaotic evil.
Most of the evil done by the left is of the lawful variety. Tree spikers or research lab bombers, for instance, believe that their violent means justify the ends of protecting forests or animals. (This would also describe "pro-life" violence, too.) You see almost no-one on the left who harms others just because they get in the way, or because they get off on it. Even the guy who shot up the Discovery channel offices thought he was acting in good faith. Hell, even Hitler thought he was doing the right thing (and here, I'll say a few "Hail Godwins".)
Ayn Rand, on the other hand, and most of her followers (direct or indirect), would be considered neutral evil. They honestly don't care about whether others are happy or sad so long as they get what they want, and what they want is money and power.
Then you have the true chaotic evils. Many of Hitler's underlings, for instance, relished the horrors they wrought. Same thing with most of the officers of the Inquisition. God, schmod. What mattered is that they enjoyed torturing heretics. Likewise, much of the anti-gay crowd? They love the idea of trying to torture the gay out of someone, or pushing them to suicide. They may sugarcoat it with religion, but that's just an excuse.
I go back and forth on Bush. If you accept the idea that he was just Cheney's handpuppet, then he might be considered lawful evil, but I think he's more neutral evil. His moral authority for what he did didn't come from an outside structure, but from his own head, and aimed toward his own self-aggrandizement. He showboated way too much to simply be in it for The Side of Right. Cheney, though... That cretin is pure chaotic evil. I think Palin is, too. Both of them get off on riling people up and fomenting violence and hatred to simply be douchebagging around for the sake of their own glory.
Regardless, however, of which type of evil is at work, it needs to be contained. We can't let these folks roam around and harm others no matter whether they're enjoying it or just think they're doing God's work. But I think if we accepted that some people simply can't be rehabilitated, and were more comfortable with acting quickly and decisively to contain those sorts, we'd more easily get to the point at which we actually can sit down and have rational conversations with our opposition, and hope to get somewhere.
Jon's ideals this direction aren't necessarily wrong. He just has yet to accept that such methods simply are doomed to fail with some people, and that many of those are currently rising in power on the right.