Sites like StackOverflow require JavaScript to work (or at least, to work in a manner approaching interactivity). So, even someone who disables JavaScript normally, would presumably enable it in order to use this popular and useful site. Furthermore – and importantly – they place trust in StackOverflow not to abuse the privilege of executing arbitrary JavaScript. That is an entirely reasonable thing for a technically savvy modern web user to do.

By serving this ad with JavaScript not vetted to StackOverflow's presumed standard, StackOverflow has violated that trust. Thus the onus is on them, not the user, to remove the offending ad or risk damaging their brand.

Honestly, what you said is like saying "why would you ever not keep a hand on your wallet" after someone got pickpocketed in a nice restaurant. Reasonable people have reasonable expectations of safety in certain places which they trust to provide it for them. No-one should go around being constantly paranoid of pickpockets everywhere, no more than anyone on the web should be constantly paranoid of malicious JavaScript even on sites with established records of safety.