Prayer doesn't bother me, per se. I don't mind if you want to pray for (whatever) at home, in church, out in public, anywhere you want, on your own. But I do take issue with teachers leading prayers in public schools, in classrooms, or at school sporting events. If the students want to say a prayer on their own, more power to them. But to have some adult authority figure call for group prayer, no, and here's why.
I grew up and went to public school in the South, in the Bible belt. Every morning in class, over the intercom, came the obligatory reading of the Bible passage of the day, and a prayer. Now, often as not, the passage read was from the New Testament, and it seemed Jesus and the 'Holy Trinity' were always mentioned in the prayer. I was aware, even then, that we had Jewish kids in school, and their religion recognized none of those. As well, from the 4th to 6th grades I was in class with a girl whose family was atheist. She was forced to sit through all this and listen to it, even though it went completely against her family's beliefs, or lack thereof. She was picked on and harassed by the other kids for quietly doing her schoolwork during the Bible reading and prayer, and for not standing to recite the Pledge of Allegiance. NO child in public school should have to be subjected to that kind of pressure and harassment from their classmates over religion.
Notice I said child. If someone wants to open a town council meeting or some such with a prayer, I don't care so much, because the attendees most likely are adult enough that if they don't believe that way, they can ignore it.