To me it is all perception. Most of us interact with people of different faiths everyday, And we have no problem.
The reputation is damaged when your getting preached at by some guy on the street corner, you see a womens clinic was bombed on TV, or were mistreated by Christians (sad but true). Its all based on that, a few can ruin your rep for the whole crowd.
Example, based on my experiences and perceptions i have a strong dislike of the Evangelical church. I throw them into the same bin as radical Islam. I know that not all evangelicals are bad people, I have evangelical friends. But as i said before, the evangelicals worry me.