I had an ex-boyfriend that would say to me "it is what it is" and I would take offense to it. As if he was implying that I should "shut up and get over it". A little overly sensitive of me, to say the least. I later realized he was simply saying that things are the way they are and that we can't control everything all the time. I no longer think of this phrase to sound rude or apathetic but as a way of giving some comfort. "It is what it is" means whatever you want it to mean.
PLEASE do not scold my grammar or general english skills. I was not an english student. I just came across this blog and felt the need to add my two cents. Thank you.