There's an underlying issue here, which is that people come at these statements with different fundamental ideas of what is
true and what are the likely
consequences of an action. Few people would actively support denying rights to other people for zero reason. Most of the time, when they believe that rights should be denied, it's because they believe that allowing those rights would trample on the rights of
other people in a significant way.
A significant fraction of America believes that allowing gay people to marry means that God will deny them entrance to the kingdom of Heaven when they die. I think this belief isn't just false, it's ridiculous - there is no God, there is no Heaven, and even if there were, He wouldn't be so petty as to deny entrance just because you supported other people having the same rights as you to get married.
But if you take this premise as given, then homophobia and all of the backlash against LGBTQ people makes a lot more sense. Which would you rather have, eternal damnation for your entire society or a few deviants being able to live their lives with each other? And I certainly can't prove that God doesn't exist and he doesn't hate gay people - I may think the ideas are ridiculous, but people who hold those ideas think that my heresy is ridiculous (and worse, dangerous - I'm certainly going to bring damnation upon myself, and probably upon those people who tolerate me). I've been told that I'm going to hell by certain more devout relatives, after all.
I think that this is the sense in which Sam thinks we should be tolerant. We need to be open to other conceptions of what is true, not necessarily what is good (and we need to learn to separate the two of them in our minds so that we can entertain different possible ideas of what is true without automatically endorsing or condemning them). Less than a century ago, it was taken as given within the Western world that God exists and the Bible is His literal word. Ideas that have challenged anything in it - like the idea that the earth revolves around the sun, or that it's more than 6000 years old - have met a violent reaction throughout history. What other ridiculous things do we believe today will be reexamined tomorrow, and how will we ever examine them if we can't countenance the idea that we might be wrong?