I've been thinking about this topic for a long time. I'm probably currently too tipsy and scattered to do it justice, but I'm going to give it a go anyway, inspired by this well-researched and insightful article about blondes in B&W horror films.
It can be kind of funny to look at the racism in old fiction, how easy it is to figure out who will be evil/stupid/cowardly. When there's almost a century distancing us from it, it's easy enough to laugh about the swarthy villains vs. the courageous Europeans in The Lord of the Rings. The African cultures represented in the Conan stories are either idiotic fodder or bestial evil, with apes in their recent or distant ancestry.
One of the most shocking examples I found recently was a story buried in the Lovecraft ouvre. You've probably never read Medusa's Coil, and I'm going to spoil it for you. You know how Lovecraft's stories often end with a shocking one-line twist, often exclaimed by the narrator, usually the most shocking revelation in a story packed with weird revelations? "Medusa's Coil" ends with one of these.
A rich southern gentleman falls in with a new age-y witch and marries her. But it turns out her hair kills people! And it turns out she's the bride of Cthulhu! And it turns out that her hair continues to kill people from beyond the veil! And then, it turns out that "though in deceitfully slight proportion, Marceline was a negress."
Seriously, if you ever wondered if Lovecraft were truly racist or just casually racist, the big twist delivered in the final line about a character who is the bride of fucking Cthulhu and whose hair fucking kills people is that she's an octoroon. Wow. Now that's racist.
Like I said, though, with enough distance you can laugh at the descriptions of slack lips and dark skin which are cues to a character's low intelligence or evil intent. Yes, "black" is still shorthand for evil, and "light" for good (I do understand that we're a species with poor night vision), but most writers have enough fear of public reprisal to avoid being overtly racist.
But physical characteristics representing moral standing are still very prevalent, and in fiction there's really no excuse for it. As the above article mentions, it's very useful for filmmakers. Lazy, but useful. In books, a writer has to go out of their way to describe a character, using the same amount of words that could be used to describe a characteristic which actually has bearing on a character's moral disposition. But it's easy to hope you share a common prejudice with your reader.
The problem is most apparent in children's fiction, where bad characters are almost always ugly (though not necessarily vice versa). Big noses, poor posture, bad skin. And this is recent. Correct me if I'm wrong, but I remember the family Harry Potter lives with being described in unflattering physical terms, at least in the early books (which are the only ones I read).
It is possible to find the opposite, though: attractive evil. But there is one physical flaw which always points to laziness, stupidity and evil: excessive body fat.
A few facts: our work has become more sedentary, and our (American) cities have been built to discourage physical activity. We are bombarded with images of rich food which instantly spark hunger. Our hormone levels are being feminized. Be it by plastic or space alien rays plotting for easier conquest, our internal environments are making it harder to carry muscle and easier to store fat. Life is becoming more stressful, and stress causes cortisol release which causes the body to store fat.
Everyone would admit that a person facing these factors is statistically more likely to be overweight than someone not. And yet, authors seem to feel totally comfortable using "overweight" as shorthand for lacking-in-character. In the past month, I've read several books in which bullies are fat kids (and are said to not even be up to bullying for being too fat!). Jack Ketchum's Old Flames is the most recent (I love his work and don't think it's the most egregious example, but as the most recent, it's the freshest in my mind). My experience was that way more bullies are fit than fat. But I'm not sure it has a bearing on the situation either way in most cases. Having abs like a loaf of challah bread doesn't make a person good--or bad.
There are points buried in this post, but I'm tired of writing, so I'm just going to say that I think the practice of using the physical to represent the internal in fiction is lazy and weird. Lazy because it's shorthand for subtle character development, and weird that a person would feel so comfortable exposing their prejudices.
"Those anuses were haunting me in my sleep!"