You have to disband the ship to get the population off of it, or use it to build a Colony or Star Base, which also disbands the ship.
Or you can get one of the survey results from Anomalies that give you a mission to build something on one of your Worlds and in return you get some some population units (normally only 1 or 2) of an Alien Race, such as the Torian Academy, Baratak Grove, Krynn Altar, Manti Birthing pool, etc, on that World.
I tried to design a Passenger ship that had both a Colony Module and a Construction Module, and built it to see if it would work as a Passenger ship.
It failed since the population remained on the ship even after the ship landed on a different World than the one that built it. The only way to get the population off is to disband the ship. I hoped that I could unload one of the two population on board like I could in GC III, but it did not work.
My test of the Passenger ship design that failed was this week (about Jan 11) using version 0.70.