I think Jennifer summed it up well.
Suffice it to say, the majority of this disagreement is based on the fact that government screwed up by sticking its nose into marriage in the first place.
Now we have all this confusion because most people don't even realize that civil marriage (which two straight atheists can have without ever setting foot in a church) and religious marriage (which is not even recognized by government on its own) are two completely different things.
The problem happened because government termed its civil ceremony "marriage" instead of something else, so now we have two different ceremonies with the same name and it makes religious conservatives really upset.
Funny, though, that you never see them complaining that we should get rid of straight civil "marriage", despite its total ungodliness. If marriage is a sacred religious ceremony, how can a purely secular governmental institution be granting any such religious benefits for gay or straight people?