I did compare Bounty paper towels and Charmin Ultra about a month ago between Costco and Amazon and found that the dollar savings I got at Costco didn't make up for having to drive 20 minutes to get there (and battle all the soccer moms for a parking space). This might not be the case everywhere and for everyone, of course, but for me I am usually willing to pay a little more for next day delivery to my door in exchange for shopping in my pajamas.
I agree that before Prime Pantry, however, that Amazon was more expensive or I had to buy way to many items (e.g. 10 bottles of shampoo).
These days, for anything non-trivial, I'll treat Amazon as the virtual storefront, then look around for competing prices, with Amazon as the last resort.
People used to think the same thing about Walmart. But so long as they have you "in the door" they will try to get you on margin. (Their margin)
But if I lived in a more urban, city environment, where easy parking isn't a given and picking up groceries in a car is more a hassle, then the time savings of having Amazon deliver for close to the same price that I would pay in store is much more worth it.
When I was in college Amazon had better prices on these products than my local stores in Iowa.
This is why I'm much less excited about Amazon than I once was.
http://www.amazon.com/Ryobi-P882-Lithium-Ion-Impact-Driver/d... - $155
http://www.homedepot.com/p/Ryobi-ONE-18-Volt-Lithium-Ion-Dri... - $150