- They cost more than the free shipping threshold, giving shipping away free
- New games are low profit to begin with
- Amazon sells enough of these that they are already in every distribution center
- Every unit Amazon ships probably arrives in a "Prime" amount of time anyway, giving away expedited shipping for free
This is just bringing some video game sales into alignment with what Amazon wanted Prime to do all along.
Amazon makes very good money on a sale that they don't control. If the costs of making that sale (or supporting returns, etc) is too high they benefit significantly by letting marketplace sellers take all the risk.