Spoilers in the post, people.
I'm not sure if much of anybody has realized it yet, but Equestria Girls undermines a common assumption of fan fiction and an attitude that appears from time to time in the Brony fandom—namely, misanthropy.
It's been played different ways in different stories: sometimes, humans are legendary monsters and nopony likes them except Lyra, sometimes humans are genuinely wicked and need to be cleaned up by being turned into ponies, and sometimes ponies have an inexplicable irrational hatred and fear of humans, or, more often, humans have a hatred of ponies.
That last one in particular I've never been able to swallow; if giant scaly monsters with big teeth landed on our doorstep, I could understand people having a negative reaction to them, being afraid or being repulsed, at least until they maybe got away and calmed down and reason kicked in and they decided to evaluate the situation more carefully. But if big cuddly plush toys with cute voices landed on our doorstep, we might be startled, but I can't imagine fear and loathing being a long-term response to such creatures, at least as long as they didn't start eating people or something. Besides that, since people actually like horses a lot in real life, and since this franchise exists to exploit that, human hatred of ponies seems implausible. This idea that humans and ponies would necessarily hate each other appears to be based on the popular notion, which has trickled down from know-nothing academics, that humans are naturally racist, which is outrageously and obviously false.
Within Equestria Girls, we see none of the reactions that fan fiction works have anticipated.
1.) When Twilight Sparkle finds herself transformed into a human, she doesn't know what manner of creature she is. This challenges the idea that humans are in any way a species known to the ponies (though this is fan-saveable, since Twilight, in spite of her vast reading, has at other times displayed plot-convenient ignorance).
2.) Twilight expresses no fear of humans beyond what would be normal for someone in an alien place and an unusual situation. She doesn't seem to much mind having a human sort-of boyfriend, either (because this is My Little Pony, which has been pulling that crap since 1987).
3.) Twilight is concerned about anyone finding out she's a pony, but she's only worried that they'll think it's "weird," not that they'll come after her with pitchforks. When her friends do find out, they're thrilled, not appalled. No anti-pony sentiments among the human Main Six.
4.) Two magic ponies travel to Humanland. Flash Sentry dates them both. Coincidence? The Deej thinks not.
"Doctor, I'm only attracted to women who used to be horses. Is that normal?"
In fact, when Flash Sentry finds out Twilight is really an interdimensional talking horse, he still wants that dance. And then afterwards he says, "Now that I know you're actually a pony and now that you have wings and horse ears, I think we should totally make out G1-style." Okay, not really. But still.
5.) The human Main Six turn into half-pony freaks. They think it's awesome. The whole school thinks it's awesome. Pony love all around.
See? No animosity between humans and ponies. Zilch. Nada. None. The closest thing to a human hater is Sunset Shimmer, and that's only because she wants to lord it over everybody, though the movie's climax reveals that she's an equal-opportunity lord-it-over-er, so even she doesn't count.