The difference being that when you go to your LGS they stock other stuff, they don't just have 1 item in the store. They promote, support, sell, introduce you to new lines, sytems, etc and are generally a focal point for the entire hobby and hobbyists.
You don't get any of that from an online only provider, you can't walk in and see something shiny and think "ooh! what's that, that looks cool!" or talk with other players (outwith your own "circle" that is) for advice, hints, tips, games, etc.
Once again, this is why more and more (including 1 very large) Manufacturers are heading toward providing to bricks & mortar only, as this will ultimately benefit all and support the hobby. It's not essential that an LGS has games tables, not all have the space necessary, but it is commonly recognised by pretty much every manufacturer that a store is absolutely 100% necessary to grow a particular line in any given area to its best effect.
Hell, if I wanted an easy life, far higher profit/income and cheap toys for myself I'd close the doors tomorrow, but I (and, to be fair, every other LGS owner I know, and I know many personally) do the job for the love of the hobby and the desire to see it grown, survive and thrive.