You can't compare a download price to an actual physical copy. The main point being you physically actually do not have anything when you purchase on download it really is totally worthless whilst many CDs depending on print and edition can often go up in value by collectors in future years. Downloads are never actually going to go up in value as you have nothing to resale. Also going in store and browsing is a completely different experience to shopping online whilst many couch potatoes want to click everything more active people actually enjoy going round shops and browsing for goods.
As for the price differences you are always going to get certain products online and in store at varying prices with promotions and sales so unless you are going to compare the entire stock of each outlet it's pointless saying this week amazon charge this compared to hmv compared to Asda. The prices fluctuate depending on attracting sales. I've paid what I thought was a great price on Amazon only to find its a few quid cheaper when I walk into Sainsbury's the following week you might see it cheaper again on Amazon.