I brought this up because it involves several topics, all of which people brought up :-) Thanks for giving me things to think about. I've got some responses/ideas - sorry if I get long winded. If you get bored you can just skim through it and read the parts that look interesting to you - that's how most people read the Bible, because it's so long

I probably should have mentioned the groups that Chic-fil-a donates to, one of which I know too well. The company donates to
the Alliance Defending Freedom, a group that in 2005 sued North Carolina Governor's School (where I went as a student and am now on the alumni board) for offering an optional, after-classes extracurricular book discussion on
"The New Gay Teenager". Some parents were angry and claimed that the school turned their son gay. Fortunately, the administration did not stand down and nothing changed, but it did put a dent in our funds and created some yucky publicity. So it's not just a free-speech issue. Sorry for not explaining that, as I didn't really know either.
So, onto the other topics:
Free SpeechMany people In the U.S. feel very passionately about their freedom to say whatever they want whenever they want. Some people abuse that right to make others miserable, and unfortunately some people listen and make it news. I find it interesting that this would have never happened if no one had put a microphone in front of the guy's face.
Anyway, the initial boycott (by same-sex marriage supporters) was a mixed bag: some were educated about Chic-fil-a's donations, some were just appalled by what the president said and didn't want to give him their business, either of which makes sense. However, the counter-protests was also mixed: some supported Chic-fil-a because they oppose same-sex marriage, and some did to support free speech. This is curious, because the original boycotters were not protesting the man's right to say what he wants to - they were simply responding to it. This has become a common trend in the conservative Christian-driven anti-gay movement: to act like victims when they are indeed the majority and in dominant political and economic power. Which brings me to...
ReligionSome of you know I am a student of ancient mythology, which includes The Bible :-p, The ancient Greeks believed in their "myths" just as much as the ancient Hebrews believed in theirs. Anywho, I've read the first five books of the Old Testament in the King James translation of the Bible, which is also the Jewish holy book. It tells the stories of Adam and Eve, Noah's Ark, the Tower of Babel, God introducing himself to Abraham by telling him to kill his son, God telling Jacob about the promised land, God guiding Moses and the other Jews out of slavery from Egypt, and then all that fun stuff about homosexuality being immoral, and finally Moses not making it to the promised land and dying. It's fun stuff, really, if you skip all of the pages that explain the lineages ("Adam begat Seth, and the Seth begat Joseph, and Joseph begat... "). My favorite part is when God makes the Earh open and swallow someone who was working on the sabbath! (the holy day, Saturday for Jews and Sunday for Christians)
Christianity (and Islam) have their roots in Judaism. The Old Testament was written in Hebrew, and the oldest copies are The Dead Sea Scrolls, which date to about 100 years before Jesus was born. There are many theories about "who" wrote these documents, but the stories in them were likely were passed down for centuries before anyone wrote them down, and the first five and most important books (Genesis, Exodus, Leviticus, Numbers, Deuteronomy) were supposedly narrated by Moses. The New Testament are the stories about Jesus, which Christians believe in and Jews do not. This is where things get tricky: while Moses's God likes people to slaughter goats and is, well, kind of crazy and violent and likes to do things like flood the Earth when people don't pay enough attention to him, Jesus talks about a loving God who wants you to be nice to each other. Jesus was executed for a reason: all of the other Jews thought he was full of crap. Ironically, they killed him (or rather, asked the Romans to execute him) not just because they disagreed with him, but simply for SAYING he disagreed with them.
A side-note: Many of the stories in the Old Testament are actually borrowed from even older stories, most notably The Epic of Gilgamesh, which is actually 2,000 years older. In Gilgamesh, the god Enlil is similar to the God of the Old Testament and floods the world in the same fashion as the Noah's Ark story, with some interesting difference in the plot. Ancient religions evolved from one another as nations dominated each other and usurped their culture, religious beliefs and traditions (consider that the Greek gods all have Roman names as well , i.e. Hades/Pluto).I read an article which suggested that the reason Judaism has survived for thousands of year despite the Jewish people being repeatedly dominated is that their God is mean to his own people. While other cultures viewed being destroyed by other nations as their gods abandoning them, the ancient Jews were convinced that they deserved it, and it was their fault for not worshipping their God hard enough.
And herein lies the bigger problem: A lot of Christians do not read the Bible - they only know excerpts, and they don't consider which half of the Bible they come from. As a whole, the Old and New Testaments can be read as a story of a vengeful God who sets up a bunch of rules and kills people for not following them, then he mellows out and loves you no matter what and just wants you to be nice to people (but if you don't worship Jesus he'll still send you to Hell). It does not take a literary scholar to see the incompatibility of "Thou shalt love thy neighbor as thyself" (Mark, New Testament) and "He that blasphemeth the name of the LORD shall surely be put to death, and all the congregation shall certainly stone him." (Leviticus, Old Testament). Yes, there are contradictions in the Bible, and this gets even muckier when it comes to politics. While ancient Judaism was a complete theocracy led by priests, Jesus said "Render unto Caesar the things which are Caesar's, and unto God the things which are God's" (meaning the government should be separate from God). But again, some people believe in the Bible but don't know what it says, which is why we have...
MarriageMarriage existed in Old Testament times, and back then it's economic and political importance could not be separated from it's religious importance because, again, the religion WAS the government (with God supposedly at the top). Marriage dictates lineages, birth rights and inheritance. The God of The Old Testament doesn't like people who are not Jewish by birth, meaning that their mother is not Jewish, which meant that it was super important for Jewish men to marry Jewish women so that their children would be in God's favor and inherit the promised land of Israel.
Marriage has evolved as religions have evolved, while until recently remaining quite oppressive to women. Currently, in 2012, in the United States of America, legal marriage (what supporters of same-sex marriage want) is a set of state recognized benefits for two people like medical decision rights, inheritance rights, parental rights, tax breaks and a bunch of other stuff. People of all religions and no religion get married to get these benefits. But because of historical affiliation, many people think marriage is something (their) God should be in charge of. I know Christian same-sex couples who have had wedding ceremonies in Churches and consider themselves married, but they do not get those state benefits.
On the whole though, marriage as an institution is falling apart at the seams. Divorce rates are sky high and the number of people getting married has fallen. In Europe, this could be attributed to increased government safety-nets eliminating the need (no need to get married for the health insurance if everyone has free health care). This is not to say that people are not coupling and settling down together, but they either don't see the symbolic significance of marriage or (like myself) do not think that married couples deserve more government benefits than single people. This is a recent trend and we are at a very interesting point in the history of this thousands-of-years-old, ever changing institution. I highly recommend the book
"Against Love" by Laura Kipnis, a serious philosophical argument against marriage and monogamy, to anyone who is still reading ;-p