Vagrant was a layer over virtualization, with hypervisors like virtualbox, kvm or vmware. The article mention virtualization and virtual machines several times, e.g. "unlike the virtual machine experience (which involved installing an entire operating system)".

For instance, deploying a complex Python application was hell, for lack of proper packaging. Using Vagrant was easy, but the image was huge (full system) and the software slow (full virtualization), among other problems. Containers like LXC and Docker were a bit easier to setup, much smaller, almost as performant as native packaging, and with a larger spectrum of features for sharing things with the host (e.g. overlay mounts).