There have been many times when those who are in charge of religious institutions have not appreciated any person going against the main tenets of their beliefs, and punishment has often been a way to keep them in line. For those who found they could not accept a particular ritual or explanation, there would be consequences. Some people simply asked innocent questions requesting clarification, but others have knowingly gone against the tide. Each type of person has often faced severe consequences, but they were much worse in the past than they are today.
The ease of mobility has lessened the ties to a particular religious institution, and many disagreements today are handled by the person changing their affiliation. It was much different in the past when people had little or no ability to travel far, and the controls over them were much stronger. These differences between the past and present have created an interesting mix of results.