The thing most people misunderstand is that God gave all of us free will, including the freedom to believe in Him or not.
If He gave us this gift, it is not up to anyone to take it away. That's where fundamentalists (of every religion) get it wrong.
Religion itself is not the problem. Any tool or organization can be made to be used for good or bad, to build, or to be a weapon. This is true of all things, everything from a hammer, to a knife, to a corporation, to a government, to a religion. It all depends on whose hands it's in. The key is to ensure that these entities are in the hands of good people, and are being used to build or improve things.