Some sellers charge a flat handling fee to feed into their profit; that is a known. If a seller charges a ridiculous amount for shipping, ebay generally intervenes. A friend of mine was contacted by ebay to question his shipping fees and required him to justify the charges.
I sell stuff on ebay, for fun. As a seller, I have been burned on shipping as in I lost money on a deal. I try to estimate shipping costs as closely as possible to actual. If I charge a handling fee, it is for packing material , boxes, tape or whatever is needed to securely box up something that was purchased. These fees are disclosed.
I would not really concern myself with a few dollars of profit to a seller for an item I really want. When you sell an item, you have the opportunity to state your handling costs. As a rule, I do not print out the package weight or shipping cost on the label to prevent folks from questioning what I did and what I charged for S&H. Since I have 100% positive feedback, I assume all of my buyers are happy.