The reason, or at least part of it, is the retail stores themselves. They didn't want online stores to be a better option where customers could save money, so they made a deal with a bunch of the publishers that they can't sell their games online for cheaper than the physical copies in retail stores or the stores wouldn't carry them.

I'm not sure how much longer that deal will last, though the publishers probably aren't in any rush to get rid of it since they make better margins on their online sales because of it (and can say "not our fault!" if people complain). But retail stores will be less and less relevant over time I think and eventually someone will want the ability to undercut other AAA games and steal a bunch of market share. Or cut out the whole physical media supply chain entirely.