I've actually run into a similar issue when sending out my packages. I make small, hand sewn plushies and started out at around 10$, but came to find that shipping them out was costing me half of my commission income.
I ended up raising my prices slightly to compensate, but it seems to have sent my business into a slump. Haven't had a commission for almost half a year now. :T
I don't go through a third-party selling site though, I advertise on DA and my Tumblr and take payments directly through Paypal.
So I'm also kind of curious if there's a better (cheaper) way.