Shipping time & cost is one of the biggest reasons why people don't buy online, or don't buy online from a given store. So while there's certainly a trick in using shipping for margin games, it really only works in places where everyone is listing at the lowest possible price like eBay -- and even then "total" price calculations make it less and less practical.
Instead of trying to profit more from shipping costs I would suggest the exact opposite and looking at how you can reduce shipping [i.e. free ground and discounted 2-day air] to pick up additional orders from your existing traffic.
Remember, marketing is a top cost outside of COGS in driving direct sales so the more of your audiance you can convert, the better you'll do with your existing spend... Plus with a strong enough shipping offer you build in another reason for people to return to you for that next purchase.