I think at some point, someone started referring to cartoon characters as "toons".

It was an attempt to distance themselves a little from the 70's/80's cartoons that had a lot more violence, inuendo, and racism. It was a time when were as a society were trying to see if we could do better by the kids. If anything I'm more confused why they called the old ones tunes. They put effort into the musical components back the, but it never seemed like a top billing kind of thing.