I think a big problem that some shops face is trying to make a decent profit off of the stuff they sell. Much more overhead at a shop then buying online, but shops still charge too much. Most shops need to get off the high price-low volume approach and go for the low price-high volume approach, much like walmart has. Charging $1000 for an amp that can be legitimately purchased online for $500 is not a problem that the consumer has to deal with. The consumer is going search for the best deal; this is something that happens in EVERY market, not just car audio. We shouldn't feel bad for "taking away business" from the local guys because we find better prices online. It's the shops responsibility to change with the market and offer services that we can't get anywhere else.
I've also heard of manufacturers that sell to wholesale houses and the like for cheaper than what they sell to dealers for. Therefore, even if a shop made ZERO profit on an amp or sub, they still can't beat some online prices. The only way to get around that is to have dealer protected products that only dealers sell. This would eliminate that problem. I know that memphis is like this.
But more companies are out to make as much money as possible, thus they will sell as much stuff as they can not taking into consideration what they are doing to the B&M stores.
The only real benefit to purchasing items from a shop is the warranty service they would most likely offer. If anyone has has tried to get an amp warrantied that they purchased online, then they know what a hassle it is. But even then, it would most likely still cost less for a person to buy an amp online and pay to get it repaired than if they purchased an amp from a shop.
$500 amp purchased online + $200 repair costs