So, I've been scanning the wiki, the game, and everything else, and I've come to a conclusion:
The cogs are trying to help.
Take this quote, for example: "The Chairman won't be happy until you are." The Cogs are trying to make Toontown a more efficent place by making them work, thinking that's what'll make them happy. Think about it. A bunch of Toons are running around like children, trashing their estates, throwing pies at each other, ect ect. The Cogs would want to try and make them happier by making them more productive.
There's also a quote directly from Joey himself. It was from reddit somewhere; Can't remember where but this one quote stuck in my head ever since I heard it:: "
"The Cogs are only doing what they were programmed to do: help toons. They're just doing it in the wrong way."
Hopefully there's some more lore for this in the future because it would be interesting.