Bootstrap has a lot of great UI components - form styles, tabs, dropdowns, etc. It looks good, it's consistent, and easy to prototype. But our client work involves highly customized design. In those cases, we don't want the Bootstrap styles, just the functionality.
But overriding Bootstrap styles can be painful. Let's take a form input field. You start by overriding the base style. But you forgot about hover and focus states, so tack those overrides on too. Then add any media query specific overrides. Do the same for any Bootstrap component you used. Finally, make sure your overrides work cross browser.
Building multiple sites with Bootstrap (and likewise Foundation) has definitely made us more aware of costs associated with customizing styles.