If the person who refers to the trans person don't know their gender, then they might be using "they/them" as a gender neutral pronoun, which it is. If they (no pun intended) do know the gender of the trans person, then they could either be protesting because they're bigoted or because they "simply" are uncomfortable. In case it's the latter, again, "simply" inform them about the correct pronouns.
I know I'm using a lot of "simply" and I also know that it isn't simple. But that's what I'd try to do.