We scientists like to think that our "way of knowing" is special. Instead of holding beliefs based on faith in invisible omniscient deities, or parchments transcribed from oral cultures, we use the scientific method to discover and know. Truth may be eternal, but human knowledge of that truth evolves over time, as new questions are asked, data is recorded, hypotheses are tested, and replication and refutation mechanisms correct the record.
So it is a very dangerous idea to consider Science as just another Religion. It's not my idea, but one I noticed growing in a set of Lakovian Frames within the Memesphere.
One of the frame is that scientists are doom and gloom prophets. For example, at a recent popular technology conference, a parade of speakers spoke about the threats of global warming, the sea level rising by 18 feet and destroying cities, more category 5 hurricanes, etc. It was quite a reversal from the positivistic techno-utopian promises of miraculous advances in medicine, computers, and weaponry that have allowed science to bloom in the late 20th century. A friend pointed out that — in the days before Powerpoint — these scientists might be wearing sandwich-board signs saying "The End is Near!"
Another element in the framing of science as a religion is the response to evidence-based policy. Scientists who do take political stands on "moral" issues such as stem-cell research, death penalty, nuclear weapons, global warming, etc., can be sidelined as atheists, humanists, or agnostics who have no moral or ethical standing outside their narrow specialty (as compared to, say, televangelist preachers.)
A third, and the most nefarious frame, casts theory as one opinion among others which should represented out of fairness or tolerance. This is the subterfuge used by Intelligent Design Creationists.
We may believe in the separation of church and state, but that firewall has fallen. Science and Reason are losing political battles to Superstition and Ignorance. Politics works by rewarding friends and punishing enemies, and while our individual votes may be private, exit polls have proven that Science didn't vote for the incumbent.
There seem to be three choices going forward: Reject, Accommodate, or Embrace.
One path is to go on an attack on religion in the public sphere. In his book End of Faith, Sam Harris points out that humoring people who believe in God is like humoring people who believe that "a diamond  the size of a refrigerator" is buried in their back yard. There is a fine line between pushing God out of our public institutions and repeating religious intolerance of regimes past.
A second is to embrace Faith-Based Science. Since, from the perspective of government, research just another special interest feeding at the public trough, we should change our model to be more accommodating to political reality. Research is already sold like highway construction projects, with a linear accelerator for your state and a supercomputer center for mine, all done through direct appropriations. All that needs to change is the justifications for such spending.
How would Faith-Based Science work? Well, Physics could sing the psalm that Perpetual Motion would solve the energy crisis, thereby triggering a $500 billion program in free energy machines. (Of course, God is on our side to repeal the Second Law of Thermodynamics!) Astronomy could embrace Astrology and do grassroots PR through Daily Horoscopes to gain mass support for a new space program. In fact, an anti-gravity initiative could pass today if it were spun as a repeal of the "heaviness tax." Using the renaming principle, the SETI program can be re-legalized and brought back to life as the "Search for God" project.
Finally, the third idea is to actually embrace this dangerous idea and organize a new open-source spiritual and moral movement. I think a new, greener religion, based on faith in the Gaia Hypothesis and an 11th commandment to "Protect the Earth" could catch on, especially if welcoming to existing communities of faith. Such a movement could be a new pulpit from which the evidence-based silent majority can speak with both moral force and evangelical fervor about issues critical to the future of our planet.