I always thought this! No matter how fast the Virtual DOM and diffing is, at it's core you are doing 2 writes. If you could just directly manipulate the DOM, that would always be faster. Really cool that someone put it into practice. I'll try it out when I have some time.
I think the bigger reason why Bootstrap is important is that it is getting designers and developers to think about style guides and modular design/code. Every application should have some sort of bootstrap-style style guide/code base of reusable elements & modules to create a consistent look and make development easier.
Bootstrap is not the first to do this and there are others like Foundation by Zurb which shouldn't be overlooked.