Aside from the pure shipping costs, you should consider adding a handling charge to the shipping fees your customers pay. After all, you need to be sure that you’re compensated for any special materials you have to purchase to package the item. That doesn’t mean you charge one buyer for an entire roll of tape, but maybe you add a few pennies to your shipping charge for these sorts of packaging consumables. And if you have to purchase a special box or envelope to ship an item, you should definitely include that cost in your shipping charge. (This argues for planning your shipping before placing your item listingwhich is always a good idea.)
When I’m supplying quality packaging for a shipment, I find that a handling charge of $1 meets with little or no objection from my customers. If I’m using free Priority Mail packaging, I charge less.
So you should have no compunction against “padding” your shipping fees with an additional handling charge. In fact, eBay’s Shipping Calculator lets you add a separate handling charge to its calculations. It’s an accepted part of doing business online.