A phobia is an irrational fear of something. An intolerance to something is usually an -ism, not a -phobia, as in
Yet people who object to homosexual practices or discriminate against homosexuals are labelled "homophobic" and their intolerance is labelled "homophobia". But homophobia should logically be an irrational fear of things that are the same (and indeed is listed with both meanings in this list of phobias) and an intolerance to a particular sexuality should surely be sexualism, sexualityism, or a similar word.
So... how did the "sexualism" meaning of "homophobia" come about? Is there another word for intolerance of / discrimination against people of a particular sexuality that doesn't imply irrationality or fear?