When I was in college, I went to the movies alone all the time because I was into edgy, artsy movies my friends weren't interested in, and I often liked sneaking into one or two movies after the first one.
I think it's sad that this is a thing, where people feel so self-conscious about going to the movies alone. It's not an ideal social situation anyway, because you'll be sitting side-by-side in a dark theater, not talking. I'm there for the movies, not to show off how social I am. And if I had to count on friends every time I wanted to see anything, I probably would've seen fewer movies I wanted to see, and I would've been dragged to things I didn't, which is a waste of time.
Admittedly, I think the only animated film I've ever seen alone is Ghost in the Shell 2: Innocence, which probably isn't the type of film you have in mind when you ask this question. I can imagine the issue of going to a theater alone that might have lots of kids in it. I can only speculate, but I imagine you'll be fine so long as you keep to yourself in that situation.