MySQL connection over port 3306 can be secure when used with the right precautions. When connecting with Sequel Pro, make sure that the connection uses a secure SSL connection, and always check the credentials you're using to log in to the database. To secure the connection even further you might want to consider using SSH tunneling as an additional layer of security. As long as you're careful and keep your MySQL settings up to date, a secure connection over port 3306 is possible.
