I think they did it in order not to duplicate make's functionality. Make is useful for partial rebuilds (when you change a single file only it is recompiled). You either use make or have to implement this yourself.
They did it because they didn't want to duplicate Ninja's functionality. It does partial rebuilds, it's been heavily optimized for just doing that, and it's a Google-created project that they're already using for other non-Bazel projects.
