I think some people misunderstand what I and many other atheists mean when we say that we want a secular government. Some people think that means that we want a specifically atheistic government, one that sets atheist ideas at the top, and relegates religion to second tier, or no tier at all. That is not accurate, so let me explain what I mean when I say that I want a secular government.
A secular government, in my view, is not an atheistic government. Instead, you might call it an agnostic government. It's a government that basically says "There are many proposed answers to the questions of gods and the afterlife, and what these answers would mean for humanity. This government takes no stand on any of those proposals. It may be that humans are reincarnated, or are rewarded or punished in a Heaven or Hell, or there may be nothing after this life. It may be there is one god, many gods, or no gods. This government makes no claims to knowledge or belief regarding any of these possibilities. Instead, this government must focus only on what it can know in this life, and deal with things as they come at us in this life, without regard to any possibilities or implications for gods or afterlifes. Thus, all religions will get equal treatment under the laws of this government, with no endorsement of any one above the others, whether explicit or implicit."
On the surface, such a stance may seem to favor atheism, but I don't think it does. For example, I'm anti-death penalty, and part of that stems directly from my lack of belief in an afterlife. I think it's unconscionable to deliberately and willfully end the life of another (without their consent), when doing so means a genuine, complete end to their existence and experience of this, or any other, world. I think I would have an easier time accepting capital punishment if I believed in some form of an afterlife, as that would mean death wasn't the end of experience. A deliberately agnostic government, on the other hand, can take no recourse to either an atheistic argument against capital punishment, nor to a theistic argument for or against the death penalty. It would be forced to deal only with what is right in front of it, and thus would have to give some other rationale for or against the use of the death penalty.
All policies and laws would be similarly limited in the potential reasons used to justify them. An agnostic government would be able to give equal treatment to a diverse panoply of religions and worldviews, in a way that a theocratic or specifically atheistic government would have trouble doing. Want to display a monument to your religion or worldview on public property? Fine, but equal time and space will be granted to other groups wishing the same thing, or no time and space will be granted to any group. Want to start government meetings with an invocation from your religion? Maybe, but again, equal time and opportunity must be granted to other groups wishing to do so, or no time is granted to any group. And by the way, in such a situation, what's wrong with a simple minute of silence? Each person can pray if they wish, or simply take that time to collect their thoughts. Hell, check your email on your phone or tablet if you want.
An agnostic government doesn't care if Little Johnny brings a Bible to school to read in his free time, so long as he's not disrupting class. The atheist can bring some other book to school to read in his free time, the Muslim can bring the Koran, whatever. So long as no one is attempting to disrupt class to proselytize for their point of view, no problem. Prayer in school? Again, as long as you aren't disrupting anything or demanding special privileges, you can pray to your heart's content.
The key here is that no one religion or religious view is treated better or worse by the government, and that people are generally left alone to practice their faith as they see fit, so long as they aren't harming others. And if anyone looks at that sentence and thinks it's a bad idea, then can you tell everyone why you think some particular religious group should be privileged above others, or perhaps treated worse? Can you tell us all in terms that will convince those who aren't a member of your own particular group? Saying something like "if we don't make God part of our government he'll punish us" isn't especially compelling to anyone who doesn't worship your particular god.