This is an old question but I came across it from Google today so figure I'd share the answer.
To RDP to AWS Windows server the .pem (private key) allows you to decrypt the Administrator password in the AWS Console. Then login as Administrator with the decrypted password.
To get the Administrator password select your EC2 instance in the AWS console, click "Connect", then "Get password", enter your .pem file here; this will give you the Administrator password, then just log in as normal RDP.
There's some good info within Amazon, such as this page "Connecting to Your Windows Instance Using RDP"
http://docs.aws.amazon.com/AWSEC2/latest/WindowsGuide/connecting_to_windows_instance.html