Jared Wilson, writing at The Gospel-Centered Church:
Public prayer is always a subversive act. I don't care if you're in the churchgoer-thick of the Bible Belt or the post-Christendom wasteland of New England: praying to the Triune God of Abraham, Isaac, Jacob, and John the Baptist in public announces to everyone that Jesus is King and our "Caesars" are not. It announces that our governmental Caesars are not sovereign and the great Caesar of Self -- or the great "Pope Self," if you prefer Luther's twist -- are not sovereign. This is a subversive act. Increasingly so in every part of the Western world.
But especially so here in the Northeast.
This means that push-back on public prayer should not surprise us. You can claim your rights and freedoms all you want; the second you declare there is a God who is sovereign over all and that his Son is the only Way to eternal life, even if you're doing it with your eyes shut, head bowed, and mouth shut, you are telling anybody who disagrees not only that they're wrong, but that they're deadly wrong. And people don't like that.
But push-back on public prayer should not deter us.
I do think American evangelicals conflate too often Christianity with American patriotism, which leads to wanting to fight battles the New Testament gives us no directive to fight. I don't know exactly where Rev. Smith is going with his final words, but the American flag is no talisman for prayer. Your prayer doesn't need it to reach God and your prayer doesn't need it to offend unbelievers. (In many cases, I would think it would be an unnecessary offense. Why insist on the flag? Just persist in prayer.)
Wilson elaborates on those thoughts a bit, so it's worth your time to read the whole thing (as well as the situation that inspired the comments).
I think the very best part of that post, though, is the two points bolded (and the bolding was in the original post): we should not be surprised when people are offended by our clear proclamation of the gospel. People always have been. We should expect resistance, persecution, trouble. While our freedom is precious and beautiful and good—and I treasure it deeply—fighting for our "rights" as Christians can (does not always, but can) obfuscate our real mandate: making Christ known.
It is good for some, perhaps even many Christians to be involved in protecting religious freedom in this country. At the same time, Christians should be known as people who are not easily offended or affronted, who are not protective of our rights, who are ultimately more concerned for others' salvation than worried about their own persecution. Again, I am not saying that protecting religious freedom is bad; I am just pleading that we not make it an idol (or, in many cases, that we renounce the idol we have already made of it).