I believe you are saying that you put the chip in the arduino, uploaded the code, then took it out of the arduino and it did not work. If that is the case then you are simply missing a couple of components that are necessary for the chip to work on its own. (Notice on the page you linked that some of the photos show it set up on a breadboard. You need those other parts too.)
http://itp.nyu.edu/physcomp/Tutorials/ArduinoBreadboard
The first three steps, plus whatever wiring your project needs, will get your running as long as you upload the code to the chip first.