Thomas Jefferson is quoted extensively on issues of separation of church and state, and that's because he put more thought into it and had more to say about it than many of the other founding fathers. His words and personal beliefs have been twisted to make points on both sides of the religious spectrum, and I think that's because he was so very moderate - and not a wishy-washy, please-everyone moderate, but a real moderate, with real, firm, reasoned beliefs that don't favor either extreme. That's rare, admirable, and noteworthy.
His feelings on religion, in a nutshell, were that everyone should be free to practice his or her own beliefs, that no one belief system should be favored over another, and that for the government to restrict or endorse any particular religion or religion in general would be to the detriment of a free country. Why that's so hard for people to comprehend these days, I'll never know. His own personal beliefs tended more toward deism, and he spoke occasionally of "Nature's God" in the sense of a higher power/Creator while, being a fan of science and engineering, rejecting what he considered to be the superstitious nature of organized religion. And yet, the government that he helped form didn't overtly endorse deism as a national philosophy on which to base laws and society. Fancy that.
The ubiquitous Jefferson quotes:
"[I]t does me no injury for my neighbor to say there are twenty gods or no God. It neither picks my pocket nor breaks my leg." -Notes on Virginia, 1782
"Believing with you that religion is a matter which lies solely between man and his God, that he owes account to none other for his faith or his worship, that the legislative powers of government reach actions only, and not opinions, I contemplate with sovereign reverence that act of the whole American people which declared that their legislature should 'make no law respecting an establishment of religion, or prohibiting the free exercise thereof,' thus building a wall of separation between church and State." -Letter to Danbury Baptist Association, CT., Jan. 1, 1802
"He who steadily observes the moral precepts in which all religions concur, will never be questioned at the gates of heaven as to the dogmas in which they all differ." -Letter to William Canby, Sept. 18, 1813
"Religion is a subject on which I have ever been most scrupulously reserved. I have considered it as a matter between every man and his Maker in which no other, and far less the public, had a right to intermeddle." -Letter to Richard Rush, 1813
Thomas Jefferson. Not a fan of organized religion, really.
But his points were good ones. "Religion is a matter which lies solely between man and his God." "I have considered it as a matter between every man and his Makes in which no other, and far less the public, had a right to intermeddle." That frees us from the interference of the government or the public, thanks much, but it also places on us the burden to be responsible for our own religious beliefs and tenets. It's time, in short, for us to start acting like grownups.
The government cannot make us be sexually responsible. If chastity is a major point for your religion, then you must, yourself, be chaste, and teach your children to be chaste, and teach them to resist the worldly temptations that would cause them to be otherwise. The world can't be expected to do anything more than accommodate your beliefs; it won't endorse them, so you have the responsibility to strengthen your own faith to make it through challenging times.
Similarly, if your religion has a specific holy day, feast, or celebration, the government cannot make everyone observe it. If that celebration is important to you, then celebrate it, and teach your children to do the same. The world can't be expected to do anything more than allow you the freedom of your celebration; it won't force others to do the same, so you have the responsibility to observe it as you see fit, even when no one around you does.
The government cannot make us adhere to the rules of a holy book. If those rules are sacred to you, then honor them, and teach your children to do the same. The world can't be expected to do anything more than accept your actions, within the bounds of civil law; it won't codify your religious beliefs as law, so you have the responsibility to live according to your own beliefs.
Religion is a very personal thing. The biggest challenge to religion and faith today is its presence in the public eye; something that should be between a person and his or her deity (or lack thereof) becomes a nationwide rallying point, a publicity op, and frequently, a Trojan horse wherein bigotry and intolerance can sneak into our system of government where it doesn't belong. Right now, it's the Christian right, but the same would hold for any religion: turning a religious system into civil law doesn't make the law sacred, it makes the religion secular. Putting on a white dress and rolling around in a mud puddle doesn't make the puddle any cleaner. The separation of church and state exists not only for the protection of the state, but also for the protection of the church.
If you profess Christianity, live by the laws of Christianity and accept civil law. Don't force your faith on other people, and don't force your faith to incorporate the secular vagaries of man-made law. If your faith endorses charity, good will, love, forgiveness, acceptance, then live by those laws. If you choose to live a life of worldly concerns, don't sully your faith by pretending that those concerns fall within the bounds of your religion. Be the best Christian that you know how to be, or don't claim to be one. From what I've read in the Bible, God has a soft spot for sinners, but he's not a big fan of hypocrites.
If you're an atheist, live your life according to civil law, logic, and the laws of basic human decency. Take pride in the fact that you've established for yourself a system of morality that doesn't rely on fear of an all-powerful parent figure, and let that satisfy you. Don't try to force it on other people, and don't criticize others for their belief in a higher power, because it's called faith and everyone has faith in something. If you have faith in, more than anything else, yourself, then be glad, and let that guide your life. Be the best person you know how to be, or don't claim to be one.
Whatever guides you, whether it's faith in one god or several gods or faith in yourself and the people around you, let that be enough for you, and then live the everliving hell out of it. Accept that no matter what your personal beliefs are, we all, as human beings, have a certain collection of kindergarten-level responsibilities to other humans, among them to be nice, to not hurt people on purpose, to try to encourage peace rather than not-peace, to help people who need help, and to leave the place pretty much as nice as we found it.
Shalom and God bless.