A hatred of gender non-conformity tends to be the outcome in a community that places a heavy emphasis on essentialized notions of maleness and femaleness.
Under that ideology, trans people are viewed as a delusional violation of nature itself. We are mad hatters who think we defy the innate essential nature of masculinity and femininity.
To many New Atheists, our transness was just another religion defying the biological reality of evolution with hair-brained self deceptive ideology.