I haven't checked the dev's actual intentions, but I'd be surprised if the misery isn't an entirely intended theme of the game. That's why the factory causes pollution, which the insects attack, earning you the aptly named achievement "It stinks and they don't like it". You're f'ing up an ecosystem with an ever growing, and maddeningly wasteful [0], contraption. Your factory is an invasive cancer of metal and plastic.

[0] The overwhelming majority of what you make gets thrown into a blender and turned into Science Juice.

I tried fucking with Factorio and watching the green world get turned into a bare brown desert full of machines was immensely depressing. I sympathized with the bugs: destroy these machines, let the world stay pleasant. I think the misery is inherent in the game already.