They did bad things with the remains of regicides.
But the legends live on about the disposal of the Protector's body. The head's location is known -- at least its general locale. But no one is sure about the ... remainder.
There's a plaque in the floor near the altar where he used to be buried, before Charles II's men dug it up, hanged it, beheaded it, and if I'm not mistaken, burned the body. There's no body left to find.