Maybe you are only counting those "heretics" killed by the Inquisition because the 3000 number is very low.
Many more than that were killed by Protestants alone in the hundred years after Luther.
See the title lof this thread. i agree that there also were many 'heretics' killed by Protestants, in addition to the enormous number of witches. It is my understanding that an entire small Swiss city was put to the sword by a combined army of Lutherans, Calvinists, and Catholics. Apparently this group of 'Anabaptists' believed that since salvation was preordained, people could commit all kinds of vices since if they were saved, vice could not harm their souls. This was something the other Protestants and the Catholics could agree on.