Referring to the U.S. President as "our commander in chief," which both Joe Biden and Sarah Palin have done recently is, as Greenwald has noted in his Salon blog:*
...much more than a semantic irritant. It's a perversion of the Constitution, under which American civilians simply do not have a "commander in chief"; only those in the military -- when it's called into service -- have one (Art. II, Sec. 2).
Worse, "commander in chief" is a military term, which reflects the core military dynamic: superiors issue orders which subordinates obey. That isn't supposed to be the relationship between the U.S. President and civilian American citizens, but because the mindless phrase "our commander in chief" has become interchangeable with "the President," that is exactly the attribute -- supreme, unquestionable authority in all arenas -- which has increasingly come to define the power of the President.
*prob. subscription-only