Totally agree! Storytelling is very powerful and a talented storyteller can make you root for someone even though you "know" you shouldn't. Whenever there is a murder mystery from the point of view of the villain--the murderer--like Columbo used to do for example, I find myself rooting for the villain and hoping they can get away with it. It is just so powerful to be shown things from a certain person's point of view, even if they are doing something reprehensible like killing someone more innocent out of greed, that you start to empathize with them.
So, I think it should not be difficult to empathize with a non-mainstream character, if they were the protagonist of a film--surely empathizing with a basically good person, who has a different skin color than me, would be easier than empathizing with a cold-blooded killer! (Although, I do watch a lot of action movies!) But, those films have to get made first. And then, someone has to say, "I will give this a try," even though on the surface it might not seem like it's "for them."
Another example I saw recently: I skimmed a review of a Broadway play called "The Cake" in The New Yorker. It's about a baker who is hired to make a wedding cake for a couple, but then discovers it's a lesbian couple and she feels uncomfortable with their business. (I didn't fully understand it, because it seems like she's friends with one of the brides, so you'd think she'd realize she's a lesbian by that point??) As the baker changes and grows to accept the lesbian couple and their business, she also improves her relationship with her own husband. The review said that the woman playing the baker was good, but that the lesbian couple was thinly drawn. So it seems like, again, it's a story focused on a mainstream character, who is faced with someone non-mainstream, and learns and grows from that encounter--yet the non-mainstream characters (the lesbian couple) are not very detailed or rich characters, reducing them to props for the growth of the mainstream character. Of course, sometimes it's just bad writing or bad acting, but it's doubly unfortunate when that coincides with cliches that diminish the non-mainstream characters.