"Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof;"
There are two dependent clauses attached to the First Ammendment's statement. The first of the two clauses promises freedom from an establishment of religion. (Those against it were, intersetingly, referred to as "antidisestablishmentarians.") The second clasue however promises the freedom to freely exercise religion.
Thomas Jefferson being less enthusiastic about religion paid particular attention to the first clause. He was behind this document for his native State of Virginia, which disestablished the Anglican Church in that State. The document, which Jefferson prized only second to his Declaration of Independence, was viewed as scandalously irreligious in its time.
On the other hand, John Adams, I mean, John Adams was more enthusiastic about religion and therefore focused on the second clause. He was largely behind the this document for his native Massachusetts. (In Article III you'll notice even channells tax money to support the "Publick Religion.")
These two precedents (no pun intended) set up their respective interpretive traditions favoring different clauses, but both clauses made it in, so neither can be ignored. The goal is a balanced interpretation that respects both clauses and lands somewhere between both interpretive traditions. The Non-establishemnt-clause/Jefferson/Virginia tradition on one hand, and the Free-exercise-clause/Adams/Masachusetts tradition on the other.
Taking all this into account the article argues that school prayer was rightfully removed because it was cumpulsory, and thus an example of establishment. But to disestablish something, does not mean (to many's dismay) to make it disappear. Instead,
"All religious voices, visions, and values must be heard and considered in the public square. All public religious services and activities, unless criminal or tortious, must be given a chance to come forth and compete in all their denominational particularity... The rise of the so-called Christian right should be met with the equally strong rise of the Christian left, of the Christian middle, and of Jewish, Muslim, and other religious groups who contest the right’s premises, prescriptions, and policies. That is how a healthy democracy works. [!!!!!] The real challenge that the new Christian right poses is not to the integrity of American politics but to the apathy of American religions. It is a challenge for peoples of all faith and of no faiths to take their place in the public forum." (Italics, boldface, and five bracketed exlamation points mine.)Perhaps the above scenario sounds odd, but it's called freedom. In other words, if you don't like what someone is saying, don't pursue the tired strategy of shutting up your opponent, instead try coming up with something better. And what if you don't like religion at all? Well then
"Turn away the missionary at your door. Close your eyes to the municipal cross that offends. Cover your ears to the public prayer that you can't abide. Forego the military chaplain's pastoral counseling... Don't join the religious student group. Don't read the religious newspapers. Avoid the services of the local pastor... All these escapes to the virtual frontier provide far greater religious freedom for all than pressing yet another tired constitutional case."
Now I understand that having to avert ones eyes and ears on occasion may not be the ideal scenario for your average atheist, but part of living in a democracy means that no one gets to have their ideal scenario. So should an atheist be ticked off by the incessant reminders that we're not yet Sweden (that most secular of nations)... they might take a tip from Chicago.