The reason people make such a huge deal their outrage against MtF folks is for one main reason:
There is nothing more shameful to a man than being perceived as a woman.
Gay folks? One of those men is taking on a "woman's role"!
Trans? "Why would a man degrade himself to be more like the lower-tier woman? — who are supposed to be subservient to men? What a disgrace to manhood! Disgusting! Who would willingly choose to be a lower species?"
Lesbians and FtM throughout history have been viewed as quaint cosplayers who will eventually be forced to submit to their societal roles.. so no biggie!
In short: women are lower on the totem.
Like many others have said here: it's based in misogyny. As are many many many issues, when you really get down to it.