being raised church of christ, and that being one of the more conservative denominations, i feel somewhat "qualified" to have some input here.
i think it boils down to this: the human brain's job is to format incoming information, process it through beliefs and blinders, then the whole of experience is "projected" to "us", whatever and wherever that is. *shrug*
one of the brain's big jobs is to maintain the status quo, concerning your subjective experience. when information comes along that challenges your world view (in this case, trans ppl being taken as evidence that either god makes mistakes, god isnt actually real, etc, nevermind the whole goldfish sex change thing built into nature and a myriad of other prime examples)
anyway, when your brain develops a "dichotomy", meaning you have two conflicting beliefs fighting for space in your head, it causes a physiological reaction similar to if you were being physically assaulted.
in essence, their (my dad, for instance) brains feel like they're actually in danger at a level underneath logical thinking, and they react/retaliate, if they're not mature enough to deal with it, anyway. the rest of my christian fam, for instance, is totes cool with it.