Reasons to include people of color; people of different faiths; mentally ill people; women; LGBTQ individuals; physically disabled people; people with CF, Down’s Syndrome, Aspergers, etc.; or any combinations of these:

They exist.

How to properly do so, if you are uncertain:

Research.  Find statistics online: talk with whichever demographic you are try to write about, and try to reflect that in your narrative.  It doesn’t have to be obvious. It doesn’t have to impact the story. It doesn’t even need to even be explicitly stated. However, make sure that the character’s story, actions, and behavior match your research.  Remember: these are actual attributes of real people: romanticizing, fetishizing, or demonizing these traits can emotionally and inadvertently physically harm these people, regardless how fantastical your story.

This isn’t to say that a villain or seductress cannot be Islamic or transsexual.  It’s saying that they’re motives, their narrative shouldn’t be drawn on the fact that they are a villain because they are a muslim; the fact that they are a seductress is because they are trans.  This is what creates negative and harmful stereotypes. Cultural, socioeconomic, political, race, gender, sexuality are more complicate and interconnected than we often realize. As a society we like to isolate them, and try to fix individual problems without realizing the entire infrastructure needs repair, waiting for it to crash and repair itself.  This doesn’t often bode well.

As a writer, you don’t want to seem ignorant.  As an illustrator, you don’t want to seem cliché.  As an film/animation producer, you don’t want to alienate potential viewers.  So don’t… Innovate.

Side note:

This also isn’t an excuse to justify historically inhumane or negative behavior by allowing your protagonist to be a vile and indecent human as if it is a marginalized group.  Though, arguably, this also can still be done properly.  [see Bojack Horseman]; however, even then a portion of the audience may condone and idolize these actions, and justify their own based on your fictitious characters.  So, be careful not to glorify it too much.