Not all of those copies were sold after Microsoft bought it.
We should note they bought it for what, $2 billion dollars?
They're not going to recoup that money for years, if at all, so they need as much as they can squeeze out of the existing product.
Considering Minecraft is what, $30 on PC right now? Even in the most literal best case scenario (100% of that sale go towards recouping the cost of the franchise) that would take upwards of 60 million sales. Since someone mentioned MC being at 54M before the acquisition, they're not even at that point yet.
I have to wonder if internally Microsoft thought they could in fact recoup the full cost via just selling Minecraft, because if so, then it's definitely below expectations.