My main problem with Clippy was not how often it would appear, but that it used a modal dialog, meaning that you cannot just ignore it, you have to explicitly dismiss it before continuing to work. It's the difference between your cat rubbing against your leg and it jumping on your keyboard. One is cute, the other is irritating when happening repeatedly.
It was designed to invoke attributions of agency. It had more than its share of literalist computer misunderstandings, but unlike the box whose malfunctions were as unintended as the weather Clippy was obnoxious.
From this 2001 article:
I, at least, found this amusing.