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Heh, now here's something I've been thinking a lot about.
First, I don't think that such a fuss should be made about things like "In God We Trust" and the mention of God in the Pledge of Allegiance. The one, you don't ever really encounter except on currency and some official seals; the other, well, no one's forcing you to say it. There were a few atheists at my high school who, when we said the Pledge, simply said "...one nation, indivisible...". It's not that hard. If you're the sort of person who gets all ferhoodled when someone else believes in God... well, you need to get over yourself. Plain and simple. Stop stepping on my right to have faith in a higher power of my choosing. Most Americans believe in some form of God. It's not like we're saying "In Jesus We Trust" or "...one nation, under Jesus...". Yes, the general implication is of the Judeo-Christian God, but there's no reason why you can't choose to interpret the mentions of God differently in accordance with your personal beliefs, or just disregard them entirely.( Cut for a tangent. )
Okay, tangent done. Now, where was I? Oh, yes, as far as the whole Ten Commandments at the courthouse thing in Alabama... Well, I don't really have a problem with it, but I can understand why a non-Christian wouldn't want that to be there. So I'm not all outraged that they were told to take that statue down. I'd not be comfortable going into a courthouse where they display Islamic religious strictures, for example, because I want a fair trial based on actual law, not religious dictates, and it's a bit easier for that to happen when there aren't blatant reminders of one religion. (Actually, I wouldn't want to be judged on Judeo-Christian religious strictures either. I just thought it was more pertinent to understanding why someone wouldn't want the Ten Commandments displayed if I looked at it from the perspective of a person going to court and seeing a display of something related to a belief system other than their own.)
As far as marriage... Marriage is, in my opinion, a religious institution and should remain a religious institution. The government should nose out. This is why I'm not for gay marriage, unless the couple is of a religion that allows it. I'm not for straight marriage either when religion isn't involved. Marriage, in every sense of the word, is a religious institution, designed solely for perpetuation of both the human race and the ideology of the religion behind the marriage. That's it. It's not about love. There's a reason that, while love has always been oft spoken of as the true reason to marry, many successful marriages start off more like two people negotiating a business contract. In fact, it used to be that you found a suitable future spouse who would be an asset to your future household and courted them with the intent of making sure they would be a suitable spouse. Then you married, and if the match was good and both partners followed and believed what their religion said about marriage, love would develop, and even if it didn't, the marriage would still be a comfortable arrangement for both parties.
I'm all for civil unions, though. Anyone should be able to get one, gay or straight. There should be no difference in rights and privileges between gay and straight couples. Essentially, what I'd like to see is the government change the legal term "marriage" to "civil union", as it relates to non-religious partnership, and end the kerfuffle. Of course, there'd be no change to the fact that if you have a religious ceremony you should also register it legally. So, someone could potentially have a marriage and a civil union, or just a civil union. I'm not in agreement with the idea that a marriage shouldn't also be made a civil union because recognising the marriage in accordance with the laws confers benefits upon the spouse and possible children that otherwise wouldn't be available, and it is not in the spirit of marriage to not do something that can only benefit your family.
I know I haven't answered the question exactly. Honestly, it's a hard thing to answer. I think there should still be some level of acknowledgement that we, as a nation, have our roots in religion. However, we shouldn't force religion on anyone, force anyone to hide their own religious beliefs because of someone else's, or try and smush together religious institutions with secular ones.