Although this line of thought is prevalent today, it seems it is not new. John Stott, writing almost seventy years ago, notes “‘Hostile to the church, friendly to Jesus Christ.’ These words describe large numbers of people, especially young people, today.” (Basic Christianity, pg. 7). So can we love Jesus and dislike the church?
In short, the answer is NO!
Jesus Loves the Church
We cannot love Jesus and dislike the church because Jesus loves the church. The Apostle Paul makes this point explicit whenever he writes to the church in Ephesus. He tells them that ‘Christ loved the church and gave himself up for her’ (Eph. 5:25). Jesus loves the church, and displayed that love in a tangible act by giving himself up for her – in other words dying, spilling his own blood for her (Acts 20:28). As the hymn puts it:
From Heav’n He came and sought her
To be His holy bride;
With His own blood He bought her
And for her life He died.
The cross is the supreme act of love, and Jesus’ death on the cross was not for individual people here and there, but for the church of God spread across all nations, tribes and languages (Rev. 5:9-10). Not only does Jesus show his love for the church in giving up his life for her; but he also displays it in waiting for the church to be presented to him in perfection in the new heavens and new earth (Rev. 19:7-9).
Turning Your Back on Jesus
In fact, even asking the question ‘can I love Jesus and dislike the church?’ reveals a dangerous presupposition in our thinking. To dislike the church is actually to turn our back on Jesus – we cannot love Jesus if we don’t love the very thing he gave his life to rescue. That means our choice of Jesus over the church is actually a choice of our opinion over Scripture, because as we have seen the Bible clearly tells us that Jesus loves the church. John Piper puts it this way:
[T]he Bible is where we meet Jesus…You can’t make him up. He is the Jesus of the Bible or he is the Jesus of your imagination. If he is the Jesus of the Bible, you take the whole Jesus. You can’t carve him up in pieces. And the whole Jesus is the Jesus who loves the church. He died for the church.
Therefore, if we say we love Jesus we must love his Word, and as a result we cannot but love his church. As Mark Dever warns, ‘if you don’t like the church, you may not really like Jesus’ (The Church: A Summary and Reflection in Understanding the Times: New Testament Studies in the 21st Century, pg. 87).
 S. J. Stone, The Church’s One Foundation, 1866.