They just don't get it. Freedom of religion means that I have the freedom to practice my own, or none, and not have to be forced to put up with one dominant religion at public functions.
I have no problem "putting up with" prayers before the meal if I attend a scouting function with my DH. I understand that group's beliefs and that I'm just a guest. I could not go if I didn't want to hear it. I just bow my head and think nice thoughts.
But at public functions that are supposed to be representative of ALL the people, an openly Christian prayer is inappropriate. It's that simple.