For the atheists I know, it comes down to two issues:
1. churches do not live up to their own values. They are boring not because they don’t have a rock band on stage (some do, and they may nevertheless be boring), but because the message itself has lost its vitality and relevance.
2. there is an element of coercion in many churches. Approval and ostracism are meted out based on the degree to which one “fits” in the millieu of the church. Many people go through a phase of their lives when they question their faith. This aspect of the churchgoing experience simply intensifies the doubt that there is any substance to religious belief.
3. have a friend or relative that is gay. Have met 3 thus far that have said that to me.
You got that right. I've seen it in Pentecostalism where you are judged as to your spirituality but whether you speak in tongues, fall down (slain), how exuberant you are in worship, to put it kindly, etc.
There are the have's and the have not's. It is a very judgmental atmosphere and I can see why people reject it.
The problem is, they end up rejecting God, not what is wrong in the local church body.