Well it supports SFTP which is FTP over SSH, rather the cp over SSH which is SCP. So you are getting the same level of security, and if you are using a client like Transmit I doubt it will look any different to you as an end user.
Or does the box you are connecting to only support SCP? If so then try CyberDuck, I've used that in the past for all my FTP, SFTP and SCP needs.