It looks like the Beta of OS X (El Capitan) breaks Vagrant.
It's reported that this is because /usr/bin is no longer writeable and anything that was previously installed there (e.g. Vagrant) is removed.
This is the fix that worked for me:
sudo ln -s /opt/vagrant/bin/vagrant /usr/local/bin/vagrant
Hat tip to pointless ramblings: http://pointlessramblings.com/posts/El_Capitan/