From what I can tell, they have slightly different aims.
For instance, Cutestrap follows BEM naming conventions and uses KSS to generate its own documentation. KSS is a nice way of generating a pattern library of your own, as you start to extend your base CSS framework.
Also, one big difference is the way they handle grids. Cutestrap grids automatically stretch columns to fill up the horizontal space and allow you to provide weights. (This is essentially a very thin abstraction on top of flexbox.) Whereas Pure grids deal more with unit sizing, more like Bootstrap.
In general, Cutestrap is more opinionated (as its tagline implies) whereas Pure offers much more customizability. I'd argue that Pure should be used more like Bootstrap, as a way to prototype complex UIs before applying more custom styling, whereas Cutestrap should be more directly used as a base for your own, custom (and opinionated) styling.
Originally I had one class with grid, direct children were rows and direct children of rows were cells, but it turned into div soup pretty quickly, so I opted for one row at a time.
http://purecss.io