You're forgetting that shows that run on HBO earn money differently than shows on network TV or movies. Movies are released in theaters where people have to pay money get a ticket; this ticket revenue goes back to the producers of the movie. Network television shows are supported by advertising; more popular shows can generate more ad revenue, which goes back to the production company. Shows on HBO make their money SOLELY based on HBO subscribers (which is money that gets spread around all HBO productions since it's impossible to know whether a subscriber is subscribing for Game of Thrones or Boardwalk Empire or the latest movies or simply for old episodes of The Wire on HBO Go).
So HBO shows aren't going to be as lucrative based solely on sharing their money between all the shows out of the subscriber pool. The way they make some money back? DVD and Blu-ray sales. They can afford to charge a premium because their content is available elsewhere, and people will pay it, in a large part because shows like Game of Thrones or Boardwalk Empire could NOT be done on network television. By limiting the supply of where you can get access to the material, HBO can inflate the price, and they'll find enough people to pay it.
Now, that said, yes, it does seem a bit exorbitant. But it also costs more to produce an episode of Game of Thrones than it does to produce an episode of How I Met Your Mother, so there should be a gap in price. Also, your typical TV sitcom has 22 or so episodes per season at 22 minutes each, which means that 10 episodes of Game of Thrones at 1 hour each is actually MORE television, despite being fewer episodes. Higher cost to produce and more actual television... yes, it should cost more than a typical DVD set for a sitcom (or what have you).