Church, organised religion as we know it today is what God reffered to as, Mystery babylon the Great, the Mother of all Harlots, and Abominations of the Earth.
He cals the churches this because they teach false doctrine and lead astray the flock.
In fact in Mat 24 Jesus tells us to leave the churches and to go directly to God.
Mat 24:15 He tells us When ye therefore shall see the abomination of desolation, spoken of by Daniel the prophet, stand in the holy place,(whosoever readeth let him understand:)
And in Mat 24:16 he states Then let him who is in Judea flee to the mountains.
In the Bible Judea often depicts the church and the mountains sometime represent the Lord, as in this case.
So in essense God tells us that in the end times,the churches are corupt and God will not be using these to save his people anymore.