Akessel raises a good point, but I think F07E knocks it out of the park in how they come across. A villain doesn't always do what they do out of malice. A great many villains do what they do for "the greater good (The greater good)" and are ultimately in the right, but end up opposing the heroes and causing misery because of it. The problem is that it was handled without a lot of nuance. Hamlin champions the cause to have Sally court-martialed, and in the very same issue was confirmed to be pursuing his own agenda. Now, if this had been kept off the table for a little while, until the characters began to question just why it was that it was always Hamlin who started things against them, then it would've been interesting, but that's not what we got.
There was also the problem that the Council were very much focused on the opinions of the public, rather than the safety of the public. If the people of Mobotropolis wanted something intensely stupid (Like, say, Naugus as king, or Nicole to be exiled), then the Council give it to them. As a result of this, there was no-one monitoring the city's systems, because none of them thought about who would actually do Nicole's job once she was gone, and Eggman was able to destroy the city's shield generator with an infiltration bot, and the city was nearly destroyed twice over, with Naugus completely failing to deliver on all of his promises to keep it safe.
Also, note that it's "The people of Mobotropolis". Not the Acorn Republic. The council had a huge habit of making decisions that would affect the whole nation based entirely on the desires of the populace of it's capital city. Nobody outside of Mobotropolis' border supported Naugus, but he was still given power over the whole nation.
Despite them supposedly all being fairly smart, all that was ever needed to convince them to do something stupid or antagonistic was say "But the people like it!" and suddenly everyone except Rotor and Elias was applauding the idea. The only people who actually had to justify themselves were the Freedom Fighters, whom the council trusted less than anyone else.
And hey, it's not like they ever paid attention to due process. A crowd cheered when Geoffrey put the crown on Naugus' head? I guess he's king now, with no actual explanations for why he'd be a good king. The people want Nicole out? Let's not give anyone a chance to explain why she's needed, just exile her straight away.
The Naugus thing really is a massive hole in the council's credibility. There are so many things wrong with his accession that it forms the single greatest display of incompetence by any leadership in the comic. And this is the same universe where Maximillian Acorn and Eggman are/were world leaders.
1) Naugus is an escaped convict who has not completed his sentence. He is thus a criminal, and should've immediately been arrested.
2) Naugus's claim to the throne is highly dubious for a variety of reasons:
-A) Nobody saw Max's promise.
-B) Max's sanity is highly debatable.
-C) It was strongly implied that he had coerced Max.
-D) Naugus has mind control powers, and thus could've brainwashed Max. However, since he doesn't try to use them on the council until the Secret Freedom arc, this point does not absolve the Council of their stupidity. "Naugus hypnotized them" isn't a valid explanation.
-E) A monarch may update the line of succession multiple times, something that Max clearly did- He made Elias the heir when he found out he was still alive, made Sally the heir again when Elias ran away, named Antoine his successor by way of marriage to Sally in the 150s, and then Elias took the throne after that, with Sally being the heir because Alexis is his stepchild, not by blood. Naugus' claim was outdated from the moment Max first changed it.
-F) All of the above is barely relevant because Max promised him the throne of the Kingdom of Acorn, a nation which was dissolved in issue 179 and replaced by the Republic of Acorn, which uses an entirely different system of government.
-G) The Republic's genesis was the Prowers' desire to avoid the mistakes of Maximillian, one of which was trusting Naugus. The council proceeded to make Naugus king.
3) The Sword of Light burns him when he touches it. This is an enormous indicator that he's evil.
4) He has tried to kill everyone in the room except Elias and Rosemary at least once.
5) His having mind control powers and the people of the city suddenly loving him would've been a huge red flag for anyone capable of joined-up thinking. However, this was an Ian Flynn story, so protagonists are only capable of that when the plot allows it.