austonia,
I don't know for sure since I don't have access to the books of CompUSA or online retailers, but my guess is that COMPUSA, being a B&M Store has much higher cost. The online store only has a headquarters, some employees, servers etc. They probably don't have their own warehouses or inventory, instead drop shipping everything thru. Ingram or something.
In addition to above, CompUSA also has salaries for sales clerks, managers etc. utilities for each store, rent for each store, property tax tax for each store etc. So the while both the online retailer and CompUSA may pay the same price for the software or whatever, CompUSA also has other cost that they have to spread among their sales so they have to charge higher prices to make the same profit.