it was an honor to be called by your first name. the family name had the function to determine where you came from, that you are the Michelangelo from this family, and not the Michelangelo from the other family. But for people that were some kind of famous and admired, it was a sign of respect to call them only by their first name. Leonardo da Vinci was called Leonardo, Raffaello Sanzio da Urbino is known as Raphael and Michelangelo was already very famous in his early 20s, so he was called only Michelangelo, because he was THE Michelangelo, no further explanation needed. so it was in some way like we know Madonna and Cher today only by their first names.

he also didn't use his last name to sign his work, he always signed with „Michelagniolo, scultore“ (scultore = sculptor).

and another sign of respect was to give them additions to their names, so Michelangelo was often called Il Divino ("the divine one"), you can imagine how famous he must have been, to be given such a name in his lifetime