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.
However, whe
lets assume that your pem file and somefile.txt you want to send is in Downloads folder
scp -i ~/Downloads/mykey.pem ~/Downloads/somefile.txt root@my.ec2.id.amazonaws.com:~/
let me know if it doesn't work