When someone is "thrown" it can mean that they're surprised or confused. "Thrown" can also mean to propel something, typically by movement of the arm or hand. A catapult is a device used to launch, or throw objects. The entrepreneur's boss was completely surprised, or confused at the entreprenur's idea for designing catapults. This joke is centered on the word "thrown" and its different meanings. 
The intelligent entrepreneur ' s idea for designing catapults meant that his boss was completely thrown .