First of all, I think it is important to know that I grew up in a Christian Church, became an atheist in high school, then converted back to the belief in God while majoring in Science in college. When it comes to these sort of conversations, I usually play devil's advocate just for the sake of learning in growing. However, you are already asking the tough questions, so I'll do my best to answer some of these the best way I know how.
Yes, according to the Bible, Jesus does not like organized religion. In fact, it was organized religion that was after Him for exposing them for their hypocracy.
It is a mystery as to why God allows certain things to happen. I do know that this life is very temporary, and the things that we see as important, are not that important in the grand scheme of eternity.
We are on this earth to help, but yet we have become selfish and hardened. Sure, God could magically make everything great...but, we were not created to be robots. We must show His love by loving others.
How do I know God exists?
When you look at a building, how do you know that a builder exists? When you look at a painting, how do you know their is a painter? I know there is a creator because I see His creation!
It would have to mean that the designer of this plan was unbelievably lazy and inept, or unbelievably callous. And cruel. And indifferent. And capricious. And that is the case with every argument for design, and every argument for revelation and intervention, that has ever been made.
To draw a parallel, people used to know about fire as a source of heat and light, but not about nuclear fusion as a cause of these same two effects: and so in those days people quite sensibly based their reasoning on the idea that the Sun was a fire, since it resembled one. We might call this the Argument from Fire. But it would be foolish for someone living today to say: "We know that fire produces heat and light: therefore the Sun is on fire: therefore the Sun is not powered by nuclear fusion."