Were there, in the time of the Prophet, the Companions, and the Caliphs, Muslims who opposed the clear rulings of Islam out of ignorance or for another reason, and what was the response to them?

Opposition to explicit Islamic rulings is of two types: First, opposition by committing a sin such as fornication or drinking alcohol. The Prophet, peace and blessings be upon him, and his companions dealt with this by admonition and prohibition, then by enforcing the prescribed punishments if the guilt was proven, while encouraging concealment. Second, opposition stemming from hypocrisy, doubt, or a sickness in the heart, like the state of the hypocrites and the Kharijites. The Prophet, peace and blessings be upon him, dealt with them by conciliation and patience, so that people would not say that Muhammad kills his companions. However, after his death, peace and blessings be upon him, this type must be dealt with firmly, and the prescribed punishments must be enforced upon them, for refraining from killing them was for a specific benefit during his lifetime, peace and blessings be upon him, to win hearts over to Islam.