Morrison critiques the ubiquitous white standard of beauty and how it negatively impacts those who do not fit into that standard. Like your question suggests, those whose appearance is the opposite of the standard are often met with hostility and derision.
Pecola desperately wants to be what she perceives as beautiful because she feels that she is ugly. Morrison explains why Pecola fixates on white beauty in the following excerpt:
Adults, older girls, shops, magazines, newspapers, window signs—all the world had agreed that a blue-eyed, yellow-haired, pink-skinned doll was what every girl child treasured.
This passage suggests that American society as a whole promotes white supremacy in the guise of prettiness. The default standard is a classically European white, and since Pecola exists far outside that standard, she is not included.
More than just society, however, Pecola’s own family regards her with hostility. Morrison states that the Breedloves accept their lot in life because “they believed they were ugly.” This represents internalized racism, whereby a group buys into the idea that they are inferior to another based on social conditioning. This is what perpetuates colorism within non-white groups, a practice whereby milder ethnic features and lighter skin tones are prized over the alternatives. Pecola, being darker skinned, suffers from the internalized hatred to which her family transfers onto her very existence.