It mystifies me.
I read Janice Raymond's infamous anti-trans book, "The Transsexual Empire: The Making of the She-Male," to try to understand how a feminist could ever push transmisogyny. And while she had some good criticisms of how gatekeeping was done, and in many places still is done, it just doesn't justify her hatred of trans people.
It looks more like victim-blaming than feminism.
Aside from that, Ron Gold, and also Lynn Baker, seem to see trans people as taking the easy way out - avoiding heterosexism and/or patriarchy by transitioning to gain straight privilege and/or male privilege.
Bev Jo seems to have a long personal conflict with Beth Elliott, but I have no idea what caused that or what to make of that.
Mary Daly and Janice Raymond were both cultural feminists, and Mary Daly was very much interested in the history of mythology. She traced a narrative of the original female - a goddess-figure - being dismembered and replaced. Anyway, it was easy to misconstrue transition as a living-out of that dismemberment, instead of a living-out of remembering.
An interesting blog post on Daly's narrative here:
http://radicalhub.wordpress.com/2011/06/19/re-membering/