Apple is always trying to prevent people from jailbreaking their devices. Luckily, they haven't gone all Sony on the hackers. That's not to say they aren't trying a few things to make the device more difficult to jailbreak. It's a vicious cycle: Apple releases new version of iOS, hackers find exploit and hack, Apple plugs hole in a new iOS, repeat.
What happened here is that iBooks 1.2.1, which launched last week adds a function that makes it unable to open books on jailbroken devices. This was discovered by a fellow at website Social Apples.
According to Dev-Team's Comex, the new software basically tries to run a small program before loading any DRM-controlled book. If a device is not jailbroken, the program will not launch and iBooks will open the book normally. A jailbroken device will run the program (this is all in the background, unnoticed by the user) and iBooks will detect that and refuse to open the book, knowing at that point that your iDevice is jailbroken.
We are sure that a fix will come along in little to know time.