While the expression maybe be somewhat overused, in its proper context, it can be a good thing. When said with a degree of humility, a sense of accountability, and without attempting to evade responsibility for one's failures, "It is what it is" can be the best thing one can say.
Usually, however, a man who says this should be forced to march through San Francisco in a rainbow halter top and pink speedo's when all the stores have K-Y jelly on back order.