| In the same line as "it's all for the best," "it's all good" has quite a positive meaning, just a poor follow-through as it's entered the vernacular. To say that "it's all good," out of context, brings up Biblical connotations of God's creation of the world: "And it was good." Deep down, this phrase intends, everything has a generally-good nature.
The problem's that you most-times don't need to say "it's all good" unless it's NOT all good.
In other words, to close the conversation or to sum up what you think you nullify the premise through a blanket qualitative statement against which none can argue. So, the statement is perpetuated without consideration to its core intent.
In theory though, philosophers like Jesus or Lao Tzu might say that it is indeed all good, every thing in the world. | 
