The main problem with religion is simple.
For some reason humans are so egotistical that no matter how "different" a background they come from, their gods somehow represent a portion of themselves.
Very few practice the notion that life itself is all that it is, a cycle or some form of spirituality that pervades our existence WITHOUT having to make a tall guy with a beard or some 6 armed woman with a funny hat in charge of it.
You can be a great member of society WITHOUT having to do so in the name or following the word of your God. You can also be an Atheist that, while you may not believe yourself, respect the beliefs of others.
The problem comes when people try to force themselves on others, or embrace dated doctrines that were created at a time when society needed them and people would not follow them unless their god said so.
Simple examples are vaccinations, the eating of pork, holy cows and other beliefs that probably started out as social or political decisions that had the name of god slapped on it and people stopped questioning it. It is like telling a kid "because I said so" when they ask why.
The problems start happening when these beliefs are either forced on others or they start putting the public at risk (vaccinations, you need general cooperation to try and ELIMINATE a disease. Polio is probably one of the best examples of this).
Some of the best religious minds on all fronts for and against are, in many cases, the ones most willing to rationally discuss the origins, social impact, and veracity of many of the tenets of religion. It is only when you get to the sheeple that you start getting people uncomfortable with something that cannot be touched, held, or glued to your dashboard and start yelling at each other as a result.
For a God that believes in loving his fellow man, there sure is a hell of a lot of hate.