Companies that do a lot of shipping usually get some sort of discount from whatever carrier they primarily ship with. It varies on volume, so some companies can charge less for shiping than others. I checked on ups.com for shipping rates before I ordered from Hops Direct, for me it was $11, but the actual price they charged me for shipping was $9, so they are passing a long at least a portion of thier discounted shipping rate. Most companies will take thier discounted rate and add a certain percentage to it (such as handling costs) when they quote people shipping prices.
One thing they could do though, if they wanted to appeal to homebrewers more is sell in amounts of 3/4 lb or 1-3/4lb. That would save more on shipping because if you order 1lb of hops, the packaging will put the total weight to be 1.1 or 1.2lb and carriers will automatically charge you 2lb shipping costs, they like to round up. I had order 2lb of hops, but was billed for 3lb shipping by UPS. If I remember correctly, the actual weight was around 2.4 lb. Of course, thier packaging methods might not allow them to deviate much on product quantities.
Depending on box weight and how much extra hops are put into each package, those who order around 5lb are getting more for thier shipping buck.