Except where the leadership of these churches are simply following the dictates of their particular religion. How can we not criticize a religion if its dictates demand inequality of the sexes, or condemnation of people for who they love, or if that particular religion dictates that only those who believe in one specific deity shall get to heaven. Sure, an individual or group of individuals probably came up with the rules modern religions abide by, but generations upon generations of people all adhering to the same thing, that's not individualistic. That's communal. That's religion at work.
Again, religion is not an organization; it requires that an individual has faith, and an individual has faith in many possible varieties. Not only this, but the organization is separate from the religion itself. The people who run the organization certainly do not simply run it for having the religion have a physical entity - indeed, this is technically impossible judging from how personal of a subject faith is. The organization often has more mortal issues, such as financial gain, publicity and attempting to quash disagreeing opinions. Not everyone who considers themselves to be a particular faith agree with the organization - indeed, religions like Judaism and Buddhism actually venture far away from a central organizational structure; not to mention the Christian sects that separated themselves from the Pope's reign.
I sorta see where you're going with this now, but I do have to disagree on the fact that religion isn't necessarily something like "the Bible", the Bible is a text written about the religion that describes stories that were passed down from generation to generation. Jesus himself redacted many parts of the old testament though, implying yet again that even though the Bible is a sort of guideline, that it does not imply that Christians must rely on it. Many do not and many support things that are outright objected against in the Bible, such as divorces, gay marriage and working on Sundays.
Ultimately, this is the problem that people have with people trying to "convert" into their way of thinking - since belief and faith is such a personal subject, people do not want to sacrifice their opinion of the universe. Conversion is not about religion but is more about controlling other people and attempting to produce a hivemind.
Just as a minor disclaimer, I'm not religious in any way, I'm simply stating that religion in of itself isn't necessarily a bad thing. What leads to problems are selfishness and conquest, which are more traits of human nature than anything.
