Normally when I sell on ebay, I charge a processing fee that is part of my shipping charges. For instance, I'll tell it to calculate shipping based on UPS ground, then add $3 as my handling fee on a modest priced item. This almost sort of covers ebay and paypal's fees.
buyers factor this in and reduce the price they will pay.
i've been selling on ebay for years and have experimented a ton--people tend to overestimate the value of "free shipping" and will pay more than they would if shipping is an extra charge.
(i.e., they might pay $50 for an item with free shipping or $42 for an item with a $5 shipping charge.)