I think the key distinction is that, for the most part, the current generation of cruise missiles are targeted and launched with a "human in the loop" - that is, a person actively makes the decision to fire the missile at a specific target. However, the autonomous weapons being debated have significantly less direct human control - they are potentially designed to simply patrol a certain area and attack anything that the weapon classifies as an enemy.
Of course, there are grey areas here - certainly there are existing missiles that can be launched without a defined target and programmed to aim for anything that, say, has radar emissions that match known enemy systems.
Of course, there are grey areas here - certainly there are existing missiles that can be launched without a defined target and programmed to aim for anything that, say, has radar emissions that match known enemy systems.