NZ Bear has the single best analysis of the entire Pledge of Allegiance issue:

But it is a big deal, and now more than ever. The man filing on behalf of his daughter shouldn't have dropped the case after 9/11 -- as some has suggested -- he should have pursued it with even more vigor. Because we are at war with religious facism --- a point that the Blogosphere, at least, has become relatively clear about for some time. We are at war with what happens when religious ideology runs amok and becomes all-consuming.

Do I think the phrase "Under God" in the Pledge is the first step towards a Taliban-like government? Of course not. But that's a strawman argument. The real argument is that if we are a secular society --- and I for one hope we are --- then we should damned well act like one. It is a matter of principle.

My own thinking on this issue went through several distinct stages. Like all schoolchildren, I memorized it and recited it blindly in grade school, fidgeting and passing notes and misbehaving like all children do (er, except for YOURS, dear reader, of course). Once I got to junior high, the Pledge didn't really come up much. So, when I heard the news that "under God" was declared to be unconstitutional, these were my thoughts:

FIRST IMPRESSION

the words "under God" are in the Pledge of Allegiance ?

*mumble*I pledge Allegiance to the Flag and the United States of America*mumble*One Nation, under God*mumble*

hey, yeah! so it is!

SECOND IMPRESSION:

So what? Isn't there a War on Terror going on?

THIRD IMPRESSION:

hey, I'm religious. Maybe I should be upset about this? I want to be under God. God is great.

FOURTH IMPRESSION:

Nah.

The overwhelming media characterization has been to scream in breathless hysteric tones, PLEDGE OF ALLEGIANCE IS UNCONSTITUTIONAL!!! To most of their credit, though, Big Media has taken a pause from scaring people to point out that Congress inserted "under God" back in the 1950s.

I see this as a kind of litmus test. Everyone on the who comes out swinging, accusing people of being antipatriotic, of being depraved, of being too politically correct - these are the partisans. Beware them. These are the ones who truly have enmity for the Constitution, and they seek at every turn to ignore it, as in the case of Jose Padilla, or subvert it. actively subvert it.

What wil happen next? It will be milked for its potential to get the right-wing to show up. The leftists will feel compelled to prove how patriotic they are. And then it will get to the Supreme Court, and the words Under God will be preserved in a 5-4 ruling. Mark my words :) So, to all of you liberals out there, get over it, you lost this battle. Marshal your troops elsewhere and fight on another day. This one's a done deal.

The Principle here is that Separation of Church and State preserves religion, not hinders it. It's the reason that America is the best place in the world to be a religious person, for example for Muslims like myself. Those who are truly offended that "under God" be removed from the Pledge on religious grounds (as opposed to political opportunists), are the ones who are weak in their faith. It's almost blasphemous to think that "under God" needs to be enshrined in the Constitution, because religion is something that transcends the works of Man. Analogously, If you put the Ten Commandments on the wall but don't practice them, you've debased them, not honored them.

some additional related thoughts:

Our currency says, "In God We Trust." That's because the phrase was inserted , just after the Civil War.

And, the Founding Fathers were not devout Christians, nor was the country founded upon Christian principles.