At least in some locations, I've found the Apple Stores aren't cutting into the sales or service workloads of the independents at all. Here in Adelaide, the customers generally seem to either dislike the customer service at Apple or the location of the store. If I can sample the machines we have come in for service, most seem to have been purchased through the large retail chains like JB HiFi or The Good Guys rather than through Apple directly.
That said, I haven't come across many independent resellers that have an online retail presence. Because Apple sets the recommended prices across the board and offers extremely low margins to resellers, it's not feasible to compete on price and with many of the larger retailers (including Apple themselves) offering free shipping, if a customer is ordering online it's a no-brainer. So many resellers these days appear to focus their web presence on end solutions and what services they can offer rather than actual product listings and prices.
MAC1's website is actually one of the better ones I've come across in this regard. There are certainly some real shockers out there.