I don't find this to be the case. There are a ton of conventions in Bootstrap, an obvious one being its variables, that are very useful when working in a team, and (in our experience) with outside contractors. I couldn't imagine giving up Bootstrap simply 'because flexbox'.
Also flexbox support in IE is still terrible, so for those of us building sites for the open-web it's a non-starter for things where a 'just doesn't work' fallback is unacceptable, such as the main site structure and alignment of core elements.
Currently I only find flexbox useful for things like vertical centering, where it's not the end of the world if the element doesn't center in IE.