It's not just that some people can't read subtext: it's that some people, some of the time, don't want to notice some of it. Subtext is great for seeing what you're looking for, and overlook what you aren't, or would rather not see. Someone who likes a book, and would prefer not to read about gay characters, is more likely to overlook subtext that indicates that the characters are gay.

A non-YA example: in the Patrick O'Brian books, what is the relationship between the two main characters? Is Stephen Maturin in love with Jack Aubrey, who he often addresses as "my dear"?