Right on the front page: "Alt-C uses Google Cloud Messaging with SSL connections to copy the text."
End-to-end encryption means it's encrypted between the endpoints - any intermediate servers just see ciphertext and never have access to the key to decrypt it. SSL just encrypts the link to Google's servers - it should be basically irrelevant since the data should already be encrypted and digitally signed.
Argh, so it is not just them, but also Google who can read your texts? What do they or Google need the plaintext for?