No, phobia means an irrational fear. A legitimate fear is not a phobia. The use of phobia in homophobia, islamophobia, etc... is their way of trying to bash those who have disdain or distrust of people for their actions or lifestyle. Someone here put it better. Islamo-odium.
Odium 1.general or widespread hatred or disgust directed toward someone as a result of their actions
Yeppers.
In fact, “islamophobic” was apparently coined specifically because those wanting to either deceive or bully into silence had observed the dishonest use of the term “homophobia”.