id_rsa.pubis a public key that you add to files of authorized_keysother hosts so that you can log in as this user. Vagrant has one, so it can be added to files on other hosts authorized_keysso that it can automatically log into the system. The one you created with ssh-keygenis for you, not Vagrant.
authorized_keys - , .
id_rsa.pub authorized_keys , ( , , ).