During the April 2010 eBay town hall (listen here) Rich from the selling team responded to a callers question about shipping DSRs. In particular to keep her costs down in shipping she has actually lost money when shipping items. Rich advised her "If you are eating some of the shipping costs, let the buyer know"
I would NEVER recommend telling your buyer that you undercharged him or her on shipping. When you tell your buyer that you lost money on shipping the item to him or her that could lead to a negative buying experience and in my opinion a higher risk for the buyer to leave you less than 5 star feedback on eBay.
If you want your buyer to know that they received a great deal on shipping I would recommend you print the actual postage amount on the label.
If you insist on letting your buyers know, let them know with positive wording. For example, you may want to say "We hope you will enjoy the great bargain you found by shopping at My Cubicle Buddies. Not only did you save money on the purchase price, you received a $2 discount off of actual shipping charges."
Whatever you do, you do not want to come across as asking the buyer for additional money to ship the item to him or her.
Remember, the key is in keeping all communication with the buyer positive, that will be the best course to ensure a positive feedback and a great buyer experience.