However, much of the confusion around such issues relates to confused idea of freedom of religion. Freedom of religion in itself does not give you a positive right to do whatever you want, irrespective of what the neutral, generally-applicable law says. It merely gives you freedom from religious persecutions and impositions by the government. As I say in a long comment:
Freedom of religion basically means that the state will not persecute you for your religion or impose a religion on you. Instead the state should simply make decisions to protect and promote the secular welfare of its citizens (i.e., their interests in this-worldly things).
It can get a little bit more complicated, but that's basically it. Sometimes a decision made on a secular basis will offend the religious or in some way constrain them, but they can't claim persecution if the state was simply acting in a religion-blind way, doing something that it would have done anyway, on secular grounds, even if the religion concerned did not exist.
Much confusion is caused when definitions of freedom of religion are used that do not start from this core meaning.
No one is being persecuted for their religion if the state, for secular reasons to do with its citizens' this-worldly welfare, makes a decision to recognise same-sex marriages in the same way as it recognises opposite-sex marriages. Nor is any religion being imposed on anyone if the state simply does this for reasons relating to the worldly interests of the people concerned. Thus, freedom of religion doesn't come into it.
However, if the state refuses to recognise same-sex marriage for a religious reason ... well, freedom of religion certainly does come into it. Public policy is then being used to impose a religious viewpoint.
At the risk of being accused of spamming, I do my best to sort all this out in my book FREEDOM OF RELIGION AND THE SECULAR STATE. In any event, the idea of freedom of religion (the state will not persecute you for your religion or impose an alien religion on you) is manipulated unconscionably in these debates. Properly understood, freedom of religion is a good thing, and it is compatible with other liberal freedoms such as freedom of speech (the state won't try to control what you say and how you express yourself). However, manipulation of the idea can give it a bad name.
Laws of general application can include anti-discrimination laws, which, among other things, protect the secular interests of people in education and employment - organisations such as schools, universities, business corporations, and individuals such as landlords are required not to discriminate in certain respects and on certain grounds. As private individuals we can, prima facie, discriminate as much as we want, however irrationally. But governments tailor anti-discrimination laws as exceptions to this where private power might otherwise be oppressive. Anti-discrimination law needs to be drafted carefully, but prima facie it is not contrary to freedom of religion if it is enacted for a secular purpose.
There is much more to say, much of it in Freedom of Religion and the Secular State, but as I say in my comment on Krauss's piece, we should stick with a pretty clear core idea of freedom of religion as freedom from state persecutions and impositions. If we don't stay anchored to that idea, we'll end up getting lost at sea.