Muffycat that is the seller's choice to charge a flat rate and it's you're choice to choose to bid on the item knowing what the shipping charge might be. Some sellers say "$5.95 for shipping and HANDLING". The handling is the cost of the packaging and the time to package it up.
So they make a buck or two in shipping charges, they are the one taking the time to find a box, find some packing material, find some tape and package it up. It can take me up to 30 minutes to properly package some of the larger items I sell.
I can guarantee you that ALL retail outlets that ship make money on shipping. I know the company I work for does; we are one of UPS's largest customers and on top of giving us extremely cheap shipping rates($3 or so for a 1 lb package vs. $6 or so they charge to any Joe Smith), they give us a rebate at the end of the year based on the volume we give them.
As I said, many times I lose money in shipping. I am not a large ebayer so UPS doesn't give me very good rates; I pay "retail" rates to ship. The calculator is not always the most accurate, but it's the only tool ebay has to offer me right now.
If you want to bid on an item, and the shipping is $5.95 and you think it should be less, then you should email the seller before you bid and ask them how it will be shipped and does that include insurance and delivery confirmation. Make them justify the $5.95 if it's that big a concern. Ask yourself what it would cost you in time and gas to drive somewhere and find and buy the same or similar item and you'll usually discover that, even if you think the shipping charge is $1 or $2 too much, you're still saving money buying it that way vs. driving somewhere.