I believe this is only true if you are performing an amphibious assault. If you are offloading in a friendly territory (moving in non-combat), then you can ignore enemy subs.
This is correct. The exact text states
…a transport cannot ignore enemy submarines to offload land units for an amphibious assault unless at least one warship belonging to the attacking power is also present in the sea zone at the end of the Combat Move phase.
One additional note: It appears that a transport CAN ignore enemy transports to offload land units during an amphibious assault.