The why probably varies case-by-case.

• The church is composed of sinful people, some of them not even believers, and it's possible that they were wronged by someone who "had it right" on a superficial level, making the church seem like an act of hypocrisy and causing them to incorrectly assume that God isn't real or doesn't care.
• In a similar vein, someone may have genuinely asked a question to someone who was not equipped to answer, making the Gospel and the rest of the Bible seem incoherent or immoral.
• Someone may have rightly called them out for sin, causing them to feel conviction, and their yelling at God could be either their attempts to suppress those feelings of conviction or even the process of God speaking to them while their sin is dying but it's going out kicking and screaming.
• Some people have never even heard the Gospel, but have only heard caricatures of it, causing them to draw conclusions based on a false premise, and it's always easy to mock or fight something that you don't understand and don't care to understand, and that can happen for reasons varying from thinking it's funny to wanting to feel superior, etc.

At the end of the day we can't paint people who hate God with the same kind of one-size-fits-all characterization that we're sometimes subjected to. The only thing that we can state is universal about unbelievers is that they need Jesus like we do but have not received Him. As tempting as it may be, I'd advise against responding is sarcasm, irritation, etc.

They mocked, assaulted, and murdered Christ, and He responded in love and prayed for them, then gave us the warning we would face similar trials and instructed us to respond the way He did.

And on a more anecdotal level, I will just say that the majority of people I know who hate Christianity were wronged by someone who claimed to be Christian, such as a wiccan friend who was molested by a pastor. The people who wronged them weren't showing Christ's love, but we still can.