Most big companies were around for a long time before Bootstrap/foundation even got started. Guess which company had existed for several years already before Twitter Bootstrap came out? If the had perfectly good in-house CSS frameworks, there's no reason to switch to Bootstrap.

Bootstrap is a cookie-cutter framework, it is significantly more bloated than in-house frameworks that are tailored to only have code for the things you need (assuming you have competent devs). The same applies for performance, modularity, and extensibility.

Those CSS frameworks only enable startups to rapidly prototype an MVP without an in-house design team. It allows them to work on what they enjoy and on what makes sense considering their skillets. It would be harder if those frameworks wouldn't exist.

On the other end, when a company grows towards maturity, it makes sense to have a design team for all their products that can experiment and design specific elements that are consistent not only between themselves but also with their branding, mission and strategy.