It's very, very hard to turn a profit at retail anymore. Even in the short time span since SoaSE first came out, the number of retailers who would even carry a retail copy of Rebellion has plummeted. Walmart is the only business left that I've seen which could even be considered to have a PC games selection; Best Buy, Gamestop, Target, etc have all essentially exited the PC games market. The economy of scale is a nonexistent problem for digital releases, but it's a very punishing rule for retail as costs rise, inflation rises, and the price of PC games remains the same, and has pushed everyone but EA, Activision-Blizzard, and shovelware right out of the retail space.
On the one hand, it sucks to see an end of an era like that. But on the other hand, indie games like Minecraft, Terraria, Recettear, or Frozen Synapse simply wouldn't have existed if retail was the only option.
