Most of the people buying iPhones nowadays are not prior Apple customers. Avid Apple users who have an extensive Apple eco-sytstem already set up often prefer to buy Apple devices from the Apple store for the experience. However since the iPhone sells exponentially more than other Apple products (iPad is catching up, by the way), most iPhone buyers are new to the Apple eco-system and do not care where they buy the iPhone from. Mostly iPhone purchases are triggered by the discounts offered.
For example AT&T recently offered $99 iPhone 5s with a trade-in at the stores or with no trade-in online and Best Buy offered $150 iPhone 5s and a trade-in offer for iPhone 4/4S. I purchased a brand new 16GB iPhone 5 from AT&T for $99 online last week. Again I would have loved to go to the Apple store to purchase an iPhone 5, but I would have had to pay $199 for the same phone with the same two year contract from AT&T. See the difference!
Hence like mentioned in the article quoted here, Apple needs to offer price match guarantees and offer substantial discounts to woo customers to the Apple store to buy the iPhone. Also these discounts will pay themselves off, if the Apple store experience creates the 'halo effect' and customers end up buying much more than the iPhone they came in to buy from the Apple store.