Public prayers and such

The other day I read this interesting article by Paul Rolly of the Salt Lake Tribune called Prayers, lies and public spectacles. I've always been curious as to why so many Mormons team up politically with the same fundamentalists that end up bashing us from the pulpit. Focus on the family is great example. They team up with us Mormons on a number of political and moral issues, yet they pull an interview from their website with Glenn Beck (Mormon), because it appears to "legitimizing Mormonism" (article). Some of these groups consider us a cult. I frankly don't get it.
I also find it interesting that many Mormons favor a government that favors religious practices such as prayers, despite that fact that Mormons are constantly being left out of such religious practices as noted in Rolly's article.
There was an interesting supreme court case that stopped the use of prayers being said over the PA system at a high school football game (article). I think many Mormons would support such a prayer. Indeed, until recently I would have. However, in this particular case one of the kids who filed suit was Mormon and not only felt left out, he was quite uncomfortable with the practice. His mom actually testified that she teaches religion at home and the school should focus on teaching her kids about the world. Amen! The kid received threats and intimidation from school officials during the court proceedings. Yes, while we may favor a state that is imbued with our religion, we must remember that elsewhere it is not. Our history should teach us what it was like to be a religious minority and we should strive to not inflict that on others.
Furthermore, the Savior has instructed us to enter into our closet when we pray, and shut the door and pray to our Father in secret. He also warns about the man who prays in public to be seen of men. I don't see how these kind of prayers can be seen in secret nor do I see that they are said to be seen of men.
I strongly favor separation of church and state. Not for the states benefit, but for the benefit of the church.