I have an EC2 instance running (FreeBSD 9 AMI ami-8cce3fe5), and I can ssh into it using my amazon-created key file without password prompt, no problem.
In your case, the user root won't have any issues. But in certain cases where you're required to login under SSH as a different user, make sure the directory you're scp-ing has adequate permissions for the user you're SSH-ing.