By bad do you mean the Crusades? Because there's ample evidence those would have happened religion or not—religion was just a tool people in power used to get land and resources.
Religion does mostly GOOD, especially today. The bad, is of course, overhyped by the media.
Number one private educator in the world? Catholic Church. Number one private health care in the world? Catholic Church. Not to mention all the work local communities do on a daily basis. I think the GOOD far outweighs the BAD.
Of course, there are some bad people that again use religion as a guise to get away with terrible things. But that's the case for literally any institution.