It's because we never hear about all the good that good religious people do - it's not newsworthy. But when extremists Muslims bomb a club, we hear about that - and we associate the religion with bad things. Likewise with Christianity, when you hear about Christians in America hurling abuse at homosexuals, or the huge conflicts in Ireland, or extreme churches such as the Westboro Baptist, we associate Christianity with the bad examples of that religion.
Basically to sum up that point, it's the extremists with fundamental views that spoil it for the average person in the religion who are actually very good people.
However, I don't believe that we need religion to do be good people. I'm an agnostic, and although raised in a Christian household I knew from the start it was BS. But my lack of religion doesn't make me a bad person. If I had enough money to do what Joe's friend did, and fly out to help an uncle I'd never met - I'd do it. I follow the (non God-central) commandments somewhat; not because I'm a Christian but because they're moral things to do - don't kill, don't steal, respect parents, respect others. And most of my atheist/non-religious friends are good people too. There's plenty of Christians in the world who don't follow the commandments - murderers, thieves, even IMO (opinion!) the pope for "taking the Lords name in vain".
So yeah, I've got no problem with anybody who's religious and unless they're bad people, although I'll disagree with their beliefs, I won't voice them.