Because he played many years past his prime, many people forgot how good he was in his prime.
His prime years were 1997-2008. During this time, he was a dominant two-way player. If people are being honest, there have been very few players in history who would have been clearly superior choices to build teams around than this version of Duncan.
From 2009-2016 Duncan was still really good, but no longer the dominant player he once was.
I think Kareem was underrated for a long time for similar reasons (the Larry Holmes version of Kareem was what most people remembered).