It's right there in the URL: "the_cup_holder_joke"
Besides, the top of the computer case, usually mere inches away from the CD tray, is a whole lot more stable, and doesn't run the risk of knocking the drink over when software closes the tray unexpectedly.
The only people who ever used the tray as a cup holder, did it for the obvious meme. Note that "holder" makes it obviously a joke since the hole isn't even big enough unless it's like a shot glass. And they were much to soft and flimsy to use as a mini table.
It didn't cause the behavior but helps bound the timeframe for the phenomena.
An article from 2002: https://www.zdnet.com/article/ive-broken-my-coffee-cup-holde...