Let me relate to you something that recently happened to me.
A secular friend said, out of the blue, said that religion has done everything wrong.
I was surprised at this because she knows that I am a Christian. I disagreed.
She, then remembered I am a Christian, and said that I get strength and encouragement from my faith, and that's a good thing. But what has the church done that is good.
Now, some of you may have agreed with her at this point, and say "nothing" or point out the mistakes that all institutional churches have made. Thus, cementing in her mind that church, religion, Christianity is all bad.
I instead said: Have you ever seen an orphanage? Who started it? Likely, a church (or as some of you say, an institutional church). Have you ever wondered why many hospitals are named after a saint? This goes back to the days where there was no government or insurance to provide for sick people. It was an act of charity from an institutional church.
She relunctantly agreed (which is a big thing because she really doesn't like religion at all).
Now, look at independent churches--have they done half of the long-term charitable acts that, say, the Catholic Church has? How many orphanages have been started by independent churches? I'd say 1/10000th of the orphanages started by institutional churches.
I am not saying institutional churches are perfect, nor that atrocities has not been committed, but it is very secular to look only at these things.