There are ways to safely connect 12V (or larger) signals to your device, but they involve adding a few electrical parts to condition the signal. They will "clip" the signal at 5V to protect the input pin. I didn't read every word, but this looks like a pretty good write-up on it all:
http://www.kevinmfodor.com/home/My-Blog/microcontrollerinputprotectiontechniques