Auto responders are great, if you know how to use them! If you get an auto responder after EVERY email sent to you, it's a problem. I, as a customer, don't want to read the same response after every message.
Heres what you do: set up your auto responder to respond to the FIRST email by the customer, stating that you have received his email and will reply within XX hours. And if he or she has any more inquiries, to send another email. They should NOT get an auto responder after the further responses and inquiries. One is more then enough, and gets the point across.