This discussion often centers around how the church should keep out of state (government) decisions because not everyone is Christian so we shouldn't make Christian laws/decisions. And usually, those calling for separation want an all-or-nothing approach, i.e. no church involvement in state business at all.
Now here's the counter to that. Isn't the government and the state supposed to represent all of the people as best they can? If so, doesn't that include the wishes of everyone, regardless of religion? So isn't it true that people, who have values influenced by their religion, have just as much say as people who have values stemming from other sources?
So we can see that it is quite silly to keep religious influence out at this level.
But what about making laws which are entirely church doctrine? Well, that would be taking things too far the other way so that people with no religious leanings are not being considered fairly. So you see, there must be a balance which includes all people, but just as it is wrong to have a church state (unless the vast majority of the population is of the same religion and denomination) it is wrong to have an atheistic state. A purely secular (supposedly neutral) state is not possible either - not in the sense most would imagine.
And here's another important point. Should the state have a say over how you worship God? Isn't every man responsible before God for his own actions? Remember that people have to individually give an account to God for their actions when they see Him on Judgement Day. This means that the state would be telling you to do things for which you (not the state) are responsible for dealing with the consequences. Religious freedom should actually be protected by a responsible state.
The main point is that the separation shouldn't be the church keeping out of state business, it should be the other way around. The state needs to keep out of church business because a man's faith is his alone before God. If you look into the history of this you will uncover the truth that this is often what they were talking about in various constitutions and writings when they spoke of church/state separation.