Vagrant vs. CLI Tools
Virtualization software like VirtualBox and VMware come with command line utilities for managing the lifecycle of machines on their platform. Many people make use of these utilities to write their own automation. Vagrant actually uses many of these utilities internally.
The difference between these CLI tools and Vagrant is that Vagrant builds on top of these utilities in a number of ways while still providing a consistent workflow. Vagrant supports multiple synced folder types, multiple provisioners to setup the machine, automatic SSH setup, creating HTTP tunnels into your development environment, and more. All of these can be configured using a single simple configuration file.
Vagrant still has a number of improvements over manual scripting even if you ignore all the higher-level features Vagrant provides. The command-line utilities provided by virtualization software often change each version or have subtle bugs with workarounds. Vagrant automatically detects the version, uses the correct flags, and can work around known issues. So if you're using one version of VirtualBox and a co-worker is using a different version, Vagrant will still work consistently.
For highly-specific workflows that don't change often, it can still be beneficial to maintain custom scripts. Vagrant is targeted at building development environments but some advanced users still use the CLI tools underneath to do other manual things.