I add the cost of all the packaging materials to the shipping cost. Shipping isn't just the cost of postage.
In 2012 I paid over $600 for shipping materials including envelopes, packaging tape, mailing labels, business cards, etc.
If someone purchases from me locally, they don't need all the packaging materials that they do when the items are to be shipped.
When I print my shipping labels, the postage price isn't displayed so unless the customer does some serious digging around, they have no way of finding out what the actual postage rate was.
However, I did have one customer complain about paying $15.00 for shipping a rather large package one time. They went to the USPS site and looked up the postage cost for the size of box (24" x 16" x 6") at the weight that was declared and then asked me why I charged $15 for shipping when the post office only charged me $13.50 for postage.
Once it was explained to them that the cost of the box and packaging was $3.50 they never questioned again.