They're claiming it's legal, but I think that is something that should even go as far as the supreme court. Sure it's intended as his signature, and used with his permission, but he is not physically signing it and the autopen does bring some misuse concerns to light. I thought that the president has to actually put his hand and his mark on a paper personally for it to become law.
Thinking about misuse, someone with an ulterior motive could put a presidential order out to our armed forces to execute prisoners or some other malicious example and the prez not even have word that happened, but it was a signed order with his sig on it... I think it should only be used for answering all those 1,000s of letters and requests for b-day cards, etc. not for legal issues that require a signature from the man himself.