It Means Continue Mission. Usually said after an interruption or hiccup in whatever you're doing. This phrase is derived using the phonetic alphabet (Military Alphabet). Instead of saying Continue Mission, Charlie Mike is said instead so everyone over the radio can understand and know what you mean.
By using the first letter of each word and converting that to the Military Alphabet you get the phrase charlie mike.
C = Charlie
M = Mike
"Our vehicle is down, we're going to Charlie Mike"