What happens if there is a need to change a design detail for mobile/desktop? Perhaps a background image is used at larger screen sizes but not at smaller ones, or a simplified logo is used for mobile. These are common occurrences, I would have thought, and I can't see how it would be possible to achieve these changes without knowledge of media queries.
My point is that in order to use bootstrap (or any other CSS framework) effectively, you do need a good understanding of CSS, as well as the rules for the framework. There seems to be a common misapprehension that bootstrap is somehow a substitute for a sound basic knowledge of CSS, and that is not the case.
Media queries may seem daunting at first, but once you start playing with them, you realise they are actually quite straightforward. They should not take long to learn.