This article is too black and white and lacks nuance. The "If you're not with us then you are against us" culture. It's binary!
Do you know everyone in J.K. Rowling's set of friends? Are you absolutely sure that she has no trans friends? She really hates all trans people?
Her opinion/belief about the boundary line between transness and womanhood differs from yours - that is all.
I have Muslim colleagues, acquaintances and neighbours. But I am also non-religious and disagree with almost all the tenets of Islam. Does that make me "Islamaphobic"?