This can be quite confusing at first because this really means the opposite of cool. When you hear this term, its really not cool in fact it couldn't be more un-cool. Often hearing this means that the person thinks what you just said is totally un-cool, gay and that they are very upset, the person may in fact want to now punch a baby.
Me: Hey can I call you right back, Mike was trying to grill and there is a flaming whore running around in our backyard now. I really need to put her out.
Adeline: It's cool, call me whenever.