Perception

I think that part of the reason people have a negative view of 'the church' is because of how it is portrayed in popular media. For the most part, it is negative - either church is presented as a scam, or it is full of whackos and nut jobs. I don't really have a huge problem with that in that most of the time it is that way for a specific reason for the plot, so it is easy to say that it is just that specific church that is a problem.
What gets me, though, is that I have never been to a church that even remotely resembles the ones I see on TV. I'm not talking the building - those are so varied that anything shown is fine. What I mean is that according to TV and movies, the people who work at churches have to wear robes or suits, unless they are a hippie church, in which case they are really out there, with holes in their jeans and playing acoustic guitar. There are usually rigid rituals, or, if it is pentecostal type church, then everyone is jumping up and down and clapping and waving their hands and clapping and being all charismatic.
My churches have not been that charismatic, and I have never attended anywhere that has required the pastors to wear robes, except perhaps when performing a baptism, and even then, only sometimes. My churches have mostly had people who are devoted but not crazy, mixed with people who are mean and petty, mixed with people who are middle-of-the-road, much like any group of people, at church or not.
That is not to say that media is always way off base with their portrayal of church. I think Seventh Heaven, a TV show, had its moments. The reverend, I think of a Lutheran church, and family was shown pretty positively, and real in the sense that they weren't perfect, but they weren't terrible people either. It tended to be a bit light spiritually sometimes, but much better than most.
And sometimes movies or shows will feature a pastor who at some point has to give a sermon, and whoever wrote the screenplay takes a chance and writes something that takes a bit of a further step - it is not so 'christian' as to offend people, but there is a great deal of truth in it. Take the movie "Keeping Mum" for example. Rowan Atkinson plays a bit of a clueless reverend in a small town British church (vicar for a small town British parish?) who is somewhat oblivious to his family - he thinks things are great, his family is having issues. Near the end of the movie, he delivers a sermon that I would not feel is out of place in an actual church, except it was a bit short...or they may have not shown all of it. It's been a while since I've seen it.
But examples like that are the exception, not the rule. The church is portrayed in such a way that if a person only experiences it through the lens of popular media, then it is no wonder that people are put off by what they see. Add to that a bad experience or two with the real world church, or real world christians and people would see no point to even give God a chance. And it is impossible to avoid bad experiences with the church, largely because it is made up of people, and people will make mistakes. No one is perfect, even in the church.
And to compound the problem, it is extremely rare, ever more rare than seeing a 'normal' church service or good sermon on TV and in movies, to hear anything but the King James Version of the Bible recited. If that was the only version of the Bible that I heard, I would be extremely put off as well. The language is archaic and hard to understand and very stuffy and almost snooty. People do not talk like that anymore, and they find it hard to understand. It is old and irrelevant to most people. Part of the problem with the church back in the day (pre-reformation) was that no one understood the Bible unless they could speak Latin or Greek, which most people didn't except for the priests. Part of the reformation was getting the word of God into the hands of everyone - publish the thing in languages that everyone knew and teach them to read so they could see for themselves. If we cling to the KJV, then we return to a day when no one really understands what is being said and the priests who study are the only ones who can read the Bible. Luckily that is not what is happening in real life, just on TV.
Somewhat of a side note - in one of my theology classes in college, the professor read a verse from the KJV that had the word 'prevent' in it. If you read the word with a modern vocabulary, the verse said that the Holy Spirit would be prevented, that is to say stopped, from doing something that it should not have been stopped from doing. Frankly, the verse did not make much sense and was somewhat sacreligious. But he then explained that the KJV meaning of prevent was 'to go before' (pre - before, vent - to go), and with that interpretation the verse made much more sense. I'm just saying.
Grasp the Nettle