Please show your configuration of MySQL Workbench. Which credentials have you used?
It works for me with this settings:
SSH Username: root SSH Key File: /path/to/vagrant/box/puphpet/files/dot/ssh/id_rsa
Have you tried to disable the rules for firewall?
yaml firewall: install: '1' rules: rMco8Q6yzyFV: port: '3306' priority: '100' proto: tcp action: accept
yaml firewall: install: '1' rules: null