Well, shouting things on the march is all well and good. From your post it sounds as though you were going through the crowd of people who were there to see the pope, shouting at them, including people who had bought children with them. That sounds pretty aggressive and provocative.

I'd be offended if you shouted the atheist cooties comment at me personally, but in this context, given the Pope's comments, I can understand. I think telling people how to bring up their kids in front of them is very offensive. I don't see a problem with bringing your child to see a visiting head of a religion, whether you belong to it or not. Obviously if we all agreed with everything there we be no protest at all! But if you want to make a point, I think it should be done in a non-threatening manner.