You may not believe this, GFT, but there are people out there who believe that any faith at all is dumb, and that the people following Jesus or any other person are idiots.
There is a certain superiority complex that these people have, because they intrinsically believe that they are automatically better than any person of faith.
These people can't accept that to a Christian, prayer isn't just something we do - it's our direct connection to God.
While I can't prove the existence of God to you, I don't have to prove the existence of God to other Christians, because they are also directly connected to Him.
So, when those people who believe they're smarter and better than Christians come to a public meeting and say they don't want prayer to be a part of it, they are coming directly between the officials and their God. This is the God who Christians rely upon for wisdom. So, when the officials need to be wisest, the atheist is attempting to cut off that connection between the Christian and wisdom.
Freedom of religion is not about the ability to stop others from doing religious stuff in public. Freedom of religion is about the ability to continue doing religious stuff in public, despite those who want to stop you.
The persecution the church in America is feeling today is nothing. It's nothing. The church in America is barely doing anything at all anyway. It's not praying, it's not believing, it's not evagelizing. For the most part, when that new mega-church is growing, it's because other churches are shrinking, not that new believers are coming to Christ.
The atheist community is just taking advantage of a situation that the church has allowed to happen to shut down prayer even further.