First of all, did you try downloading a new VM? Maybe the VM failed to initialize properly, and is a very specific issue that might be solved by re-creating it.
If not, could you check if the password in
~/bitnami_credentials work for using MySQL? You can run MySQL with (replacing PASSWORD):
mysql -u root -pPASSWORD bitnami_edxapp
If so, it's likely an error with the edX setup as mentioned above and you can change the credentials with:
sudo /opt/bitnami/apps/edx/bin/python.edxapp manage.py lms changepassword user --settings=bitnami