With Bootstrap you can just pick the parts you need (so there is no practical 'overhead'), and most sites will at the very least need a responsive grid, and Bootstrap's (3's at least) is excellent. I don't know why you wouldn't want to use it, or something very similar from another framework.
Even with flexbox you'd still need to reimplement the 'different column behaviours at various breakpoints', which is non-trivial.
Also there's the whole other-devs-understanding-your-code scenario 'oh this is Bootstrap, I know this'. It gives you conventions BEYOND just what raw CSS gives you, e.g. the Sass variables it exposes.
