I agree with the comments that stores have to 'justify' the cost of boxing, labeling, packaging, cutting, etc. But isn't what they can (should?) make up in their markup or their margins?
I work in an industry where there is a lot of labor invested in packing, pulling orders, handling product, etc... we don't charge 'extra' for handling fees because that's part of the overall business expense. Someone could come in here and pull and pack their own product, but it's no more or less money if they do it or we do it. I think it comes down to customer service...
I would order online all day long (hehe! you know what I mean) if there were no shipping charges. I would rather know EXACTLY how much something is going to cost when it hits my door step- even if that means adding a little into the price on the business' end.
That's my 2 cents anyway. :)