But for user-facing stuff, designers and PMs want to tweak everything about the interface, and by the time you're done, you've rewritten most of the CSS and you actually spent more effort doing so than had you just written the CSS yourself the first time.
Also, the way you wrote it ends up being a frankenstein-esque collection of style overrides. Zurb foundation is notorious for requiring hyper-specific CSS rules to override their default styles.
Bootstrap has made some progress towards making it more tweakable, but if you're maintaining/customizing an app long-term, you're better off writing your own css for the most part.
Edit: to add to that, the biggest problem that bootstrap solves IMO is a standard grid system, of which there are now many, more composable grid systems to choose from. Grid systems are so basic that its probably fine to pull one from the shelf, but with flexbox its really not that hard to write your own anyway.