J.C. Ryle here is telling us that we need to have private devotions with our Lord, and not simply go to a "Church" that has all the popularity of the day.This is the root of which He speaks. Jesus is the root isn't He; through the Holy Spirit.
Jeremiah says: "Blessed is the man that trusts in [ public & private] the Lord, and whose hope is the Lord.
For he shall be as a tree planted by the water, and that spreads out her roots by the river, ...her leaf shall be green; ....neither shall she cease from bearing fruit!" (17:7-8)