This seems like such a silly question, that people would even think such a thing, yet it seems to be a common problem these days.
Yet it is understandable, people get hurt; they’re offended and turn away from the church. The church is not claiming to be perfect, yet the people who say they “hate the church” are obviously dealing with some issues of there own. That is why we need the body of believers to help each other through these issues. You can’t just run away from your problems and think that will fix it. You are only left with bitterness and resentment in your heart, which solves nothing. You are still left hurting and without a family to go to.
It’s not right that it is a problem, but unfortunately it is.
The “church” in the original Greek is defined as the ones who “belong to the Lord”. If you love Jesus but hate the church you are disobeying the Word. First of all, you hate something that the Lord loves. From Psalm 97 derives a popular quote, love what God loves and hate what He hates. He hates evil, but loves his bride, and if you hate His bride… you do not love what He loves. Secondly, you are disobeying the second commandment, “You shall love your neighbor as yourself”(Matthew 22:39). Where in hating the church does loving your neighbor reside? Nowhere.
You are deceived if you think you can hate something that God loves and desires to be with forever. The church is not the problem, you are.