Essentially the same thing has happened here, but in the digital realm. A thief (or thieves) broke into the backend systems of an exchange which was holding bitcoins for its customers, and the thief stole all their bitcoins. The exchange and/or its customers have suffered losses, but every single bitcoin stolen by the thief will continue to be as valuable as any other bitcoin. In other words, Bitcoin will continue to be the same exact commodity -- its integrity has NOT been compromised.
The moral of this story: if you own bitcoins, make sure they are stored in a truly secure system. Many Bitcoin exchanges claim to be -- but really aren't -- truly secure!