Within Ruby on Rails applications database.yml is a plain text file that stores database credentials.
When I deploy my Rails applications I have an after deploy callback
Even if you secure the database.yml file, people can still write that uses the same credentials if they can change the code of your application.
An other way to look at this is: does the web application have to much access to the database. If true lower the permissions. Give just enough permissions to the application. This way an attacker can only do what the web application would be able to do.