I'd argue that you're right that there's nothing intrinsically disparaging about ilk as a word, but in contemporary usage it does seem to have become quite negative. I know the dictionary doesn't say it, but in my discussions it seems to have shifted towards the negative.

Consider this: "Firefighters and their ilk." It's not a word that nicely described a group, even though that's what it's supposed to do. I think the language has moved to where we just say Firefighters now when it's positive, and ilk or et al when it's a negative connotation.

Just my experience.