Actually the only ones who don't get how time travel works are the writers. Jack returned AFTER he left, not before. What does this mean?
It means that all of the events in the future were required, through causality to occur. Jack arrives>Future events>Jack returns. If jack had arrived before leaving it would have in made everything, but he didn't.
So then, logically, where is everyone.everything? It's a causal loop, force reconciled as a new branch timeline; the moment Aku is defeated.
Make a line, at the end of that line, start a loop. Continue the loop all the way back and past the original point, and restart the line. That's the original timeline.
Now, at the point, in the past, but AFTER Jack has left, continue the end of the loop as a straight, dashed line. This represents the future timeline continued after Aku is destroyed. Presumably, everyone just watched future Aku blip out; and are gonna start cleanup.
Of course you cry, "If Aku doesn't exist, how do we have future events with Aku?" Again, causal loop. The events became necessary for Jack's return, because he never negated leaving in the first place; so they had to happen.
That creates a paradox with the original timeline where they can't happen after Jack returns. The only way to achieve both is with a new timeline, born of the history of Jack's original timeline, spliced with the causal loop, and continuing, without Jack; after Aku's defeat.
Therefore, no one except Aku should have gotten erased. Not Aki, not the other characters, no one. This may seem needlessly laborious observation; but truly, the ending offended me once I thought about it.
It was a cheap attempt to shove a needlessly bittersweet "noble sacrifice" into the ending. It ignored the basic concept of time as a function of necessity or causal action; and it produced an ending the didn't fit.
But rejoice, maybe there's a timeline out there where the writers got it right.