Short answer, the unit is eliminated. APC's have only one step, thus if the APC loses a step, the unit it is carrying is eliminated.
The
rule reference is 5.65:
If a transport unit is fired on, everything it is transporting suffers the same fate as the transport. If a transport must make a morale check due to enemy fire, make one roll for the transport only, adding the morale bonus of any one leader it is carrying or in its hex or an adjacent hex. If the transport becomes disrupted or demoralized or is eliminated, so does everything it's transporting.