I don't really label myself to a certain sect, though I do go to a baptist church, and this is my rebuttal:
We're supposed to worship collectively and hear teachings from God's appointed leaders. Jesus wants us to break bread, together, in remembrance of Him (not just in practice, but in worship also). We are the body of Christ, brothers and sisters in Jesus, and being a member of the body, we need to incorporate ourselves with other members and become part of the family; not cut ourselves off. When one part of the body isn't getting it right, you can't blame the entire body. But it is our job to set them straight. We need to be there for each other to build each other up in love, faith, motive, knowledge/wisdom/understanding of God's Word, etc., and this is done within the church. People use the word "religion" to define such things..
When the guy in that video talks about religion, he seems to be referring to people who practice over worship, and have motives of self interest, and that is what he should say. He shouldn't refer to it as "religion". There is much Christian religion out there that are 100% in it for Christ, and this guy doesn't acknowledge that and makes religion as a whole look foolish.
Here is a cool rebuttal video from a Lutheran guy: http://www.youtube.com/watch?v=TbsadOQK_6A