The following is based on the Soviet campaign of Red Alert 2 and might contradict canon.
I wanted to introduce to you my little friend. This is Sam, like Uncle Sam. Say hello, little uncle. The Americans, they have turtle in children's film, it teaches them to fear Soviet Union. The little turtle sees big Russian missiles coming, and he ducks and he covers. "Duck, cover!". - Alexander Romanov(src)
He was named after the American propaganda icon, Uncle Sam. While introducing Sam to the Commander, Romanov referenced Duck and Cover!, a children's educational film that was played in American schools during the real-life Cold War on what to do in case of an nuclear attack. An animated segment of the presentation featured a turtle named Bert.
Sam does not like to be petted on the head, despite Romanov doing so repeatedly.