Personally, I think Amazon is great. You can research, maybe read an excerpt, and then order easily, often at a discount. If a title is out of print, there's always half.com. Otherwise, you can order just about anything, and you almost never have to worry about sold-out titles. Come on, how many times have you wanted to get into a series and nobody seems to have the #@*^%@ first title in stock?
This applies just as well to super-stores as it does to small independents. It's a matter of sales and shelf space. I worked as the fiction supervisor at a Barnes & Noble for a while, and I was frequently reminded that we were running a bookstore, not a library. Certainly, we had a better selection than a mall store, but there were so many titles I just couldn't believe we didn't carry, or we only carried 1 at a time. Still, I feel I was able to offer customers something like the level of service that people praise independents for. I just wish I could have had Amazon-like resources at my disposal (special ordering is just such a mess for most people).
Maybe I like Amazon because for me, it's just a useful supplement to my bookstore habit. I live within walking distance of 5 used bookstores, and Barnes & Noble and Borders are both less than 10 minutes' drive away, so I can easily indulge my incessant urge to browse. Much as I love finding cool new titles online, it's even better to grab a book off the shelf and get so absorbed in it that I just can't put it back.