"It is what it is" is the verbal/written equivalent of a non-committal shrug of the shoulders; a way of saying nothing is going to change the situation. Depending on the context of the conversation and the parties involved it can be a statement of sympathetic resignation towards or about someone experiencing something that is totally beyond their control or it can be a euphemistic manner of saying "tough shit it's going to happen no matter what you say or think." In so far as language goes it virtually leaves the communicative-recipient with nearly complete responsibility to apply/supply an interpretation to its contextual use. I, for one, thoroughly dislike its use and would just as soon never encounter it again.

It was used in a text message to me in response to a situation to my response to a situation someone I care about was getting herself into, as she was kind of annoyed with my protective attitude, the bottom line being, as I understood it was that she is going to do what she is going to do no matter how concerned I am for her safety. My text response was to counter her cliche-excuse with a truism, as seen below:

She: "it is what it is"
Me: "It's hard to not be one's self"