How Do You Secure database.yml?
Take a look at this github solution: https://github.com/NUBIC/bcdatabase. bcdatabase provides an encrypted store where the passwords can be kept separated from the yaml files.
bcdatabase
bcdatabase is a library and utility which provides database configuration parameter management for Ruby on Rails applications. It provides a simple mechanism for separating database configuration attributes from application source code so that there's no temptation to check passwords into the version control system. And it centralizes the parameters for a single server so that they can be easily shared among multiple applications and easily updated by a single administrator.
The way I have tackled this is to put the database password in a file with read permissions only for the user I run my application as. Then, in database.yml I use ERB to read the file:
production:
adapter: mysql
database: my_db
username: db_user
password: <%= begin IO.read("/home/my_deploy_user/.db") rescue "" end %>
Works a treat.
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.
You'll also want to make sure that your SSH system is well secured to prevent people from logging in as your Capistrano bot. I'd suggest restricting access to password-protected key pairs.
Encrypting the .yml file on the server is useless since you have to give the bot the key, which would be stored . . . on the same server. Encrypting it on your machine is probably a good idea. Capistrano can decrypt it before sending.