"A Confederacy of Dunces" struck me much more as a chronicle of weird people and their foibles with a large dose of regional flavoring--sort of like Napoleon Dynamite but focused on a city underbelly.

I don't remember "fatness" being a signal of evil, and I don't remember any of the non-fat people being any better than the fat ones.

However, it has been quite a while since I read the novel, and I really didn't like it very much. So, my memory may be faulty, and your mileage may vary.