if you look at the specs for a chip, you'll see "absolute maximum ratings". This means that the chip is ALWAYS SAFE below these voltages/currents. The ATmega chip is rated for up to 6V operating voltage, and the input pins can go 1/2V over the operating voltage, or as low as -1/2V.
Typically you are operating at 5V, so you can safely apply up to 5.5V on a pin. That does NOT mean that you will automatically fry the chip if you put 6V on an input... It means that you MIGHT fry the chip, so you should NEVER do it. 
Where I work, we make a board that operates from 5V, and of course it has lots of 5V chips on it. One of the configurations has the same barrel-connector as our 12V products... So once in awhile, we accidenly plug 12V into it... Usually, that frys the board... But usually just the RAM gets fried, and sometimes the CPU chip. Everything else survives, and we can repair the board by changing one or two chips.