In previous centuries, religious institutions were often supported by governments. This factor provided them with the means to exercise religious control over large populations, and they were often able to control even those in charge of the governments. Combined with the lack of ability to travel very far, many people were at the mercy of whatever religion was declared legal throughout the land. They knew that failure to be part of that system could see them banished to a faraway place where they would be unlikely to survive.
Banishment was often a death sentence, but there were worse punishments to be had in some religions. The Amish have become famous for shunning those who do not follow their rules, and it is a traditional form of control that remains in place today. When a person is shunned, no one in the community is allowed to acknowledge their existence with the exception of their family. Even those people can only acknowledge them while at home, so they are still at a loss when they are in public. It is a very effective means of maintaining control over members.
The majority of people in the modern world do not face these types of punish as a death sentence, and they are often able to move to a place where their views are accepted. Many religious institutions have sprouted branches all over the world, so finding a new church and congregation is often easier than remaining within an area where questions are not tolerated. Keeping in touch with family and friends is also easier through electronic communications, so that avenue is unlikely to be shut off by a religious difference.
Most modern governments are less concerned with spiritual affairs, so most religious leaders have little or no control over them. This allows people living in an area to be able to worship how they want, and there is much less control over their daily lives due to this factor.