My issue with religion has always been the behavior it spawns. If you think about the universe (meaning EVERYTHING), you can divide it into two major categories between the subjective and the objective, or more simply, the idea and reality; genotype and phenotype; information and action. Everything resides in this duality. Too often in our history the idea (religion) often leads to a awful behavior (Crusades, Jihad, Inquisition, etc.).
But maybe this is not true. Maybe religion, whether Christianity or whatever you want to call it, leads to benign or even positive behavior. Most theists will obviously not start religious wars or engage in violent crime.
So really, it's the premise of belief I disagree with, but we could argue premises all day and get nowhere. Our action, our behavior - these things matter because our thoughts and motives can only be inferred, never completely deduced. The only concern I would have is how deep one's faith might be. Because unthinking faith, no matter how strong the cause, is a dangerous state, as people, no matter how noble or well-intentioned, will abuse that power. And then history repeats itself.