There are so many many ways to interpret the Bible. Each sect of religion has decided to interpret the Bible in their own way, that is what makes them different. I find it hard to believe that there is only one way to worship God. Religion has become too secular and distant.
The difference between past historical "votes" on key doctrinal issues in the Christian religion and current discussion over the Church's response to cultural change is night and day. One clear reason you can say that the religion, especially in the Christian Church, is more tolerant is the fact that you are not killed if you disagree. Even over the issue of infant baptism in the 16th and 17th century, you personal health was dependent on which side of the issue you came down on. Now day disagreeing groups just split and go on their way.
Compared to what it was long ago, religion has grown considerably more tolerant. Things that once would have been severely punished, such as immorality and blasphemy, are now often accepted. Even the practice of voting to decide the divinity of Jesus Christ points to greater tolerance. Voting points to a willingness to consider and adopt other opinions.
In this age of religiously motivated terrorism, it is easy to think that religion overall is intolerant. However, the pluralistic societies of the Western Hemisphere and Europe - where religious diversity is accepted and the main religion, Christianity, no longer engages in repressive events like the Inquisition - show that different faiths can exist comfortably together. While religious conflicts still are found around the globe, many of these - like the Muslim/Christian fighting Nigeria - have as much to to do with ethnic identity and the distribution of political power as they do with faith. While there are certainly areas where religion is repressive (e.g., the areas of Syria and Iraq controlled by ISIS) religions in general are becoming more tolerant of other faiths.