It's a tough situation really.
I don't mind paying a little more to shop locally -- and I always account for S&H charges in this. But the price diffs are often quite large though.
Still, I'm not really (often) choosing Amazon over J&R or Best Buy or similar when the latter run reasonable sales. Amazon's prices are generally just competitive, but not exactly a big undercut vs relatively big stores (or chains) like J&R and Best Buy -- when they are, it's usually because the latter are charging full retail or very close to that, which is just too high in most cases. And I pay sales tax in both cases. I've been just as likely to buy BDs, DVDs and CDs from J&R and Best Buy as from Amazon. And until more recently (when I finally subscribed to Amazon Prime), I wasn't paying Amazon for shipping -- and I'm getting more than just free shipping w/ Amazon Prime.
IF they can work out a business model that makes them consistently (reasonably) competitive vs Amazon, that may be good enough. Problem is they are not consistent. And of course, the recession plus new competition from streaming plus often relatively high price for essentially recycled-yet-again catalog titles don't help.
In J&R's case, I suppose the problem may also be partially attributable to the changes that have been taking place in downtown Manhattan, which is connected to the recession as well as the still-ongoing redevelopment since 9/11 (and the resumption of skyrocketing cost of real estate). Sounds like they're hoping to reboot into something that fits in well w/ the changes going on (both locally and online). In a sense, they need to reinvent themselves much like B&H did more than a decade ago when digital (and online shopping) replaced film (and much of local shopping). J&R's overall business has really been not quite that much different from B&H's other than (prerecorded) media sales being a big part of theirs. Perhaps, they will refocus and completely drop media sales (and maybe their lightweight attempts at household appliances too) to be more like B&H... which would be a bit sad, but perhaps, inevitable...