I believe Clarice, the FBI profiler specifically says that Buffalo Bill just thinks he is transgendered, and then says transgendered people (she actually says transsexual, but back then that was the accepted jargon) are not particularly violent. And Buffalo Bill is a composite of some very real, and notorious serial killers.
As far as I know Thomas Harris researches very well, he even includes the bit about specific hospitals that do sex-change surgeries. So, yeah, it is not transphobic, unless you are really looking for a subtext. But the subtext was transformation (i.E. Clarice will transform into a real FBI agent, and Bill won't transform into a woman because he isn't really a transgendered person just hates himself, and thus will never stop killing women).
For it to be Transphobic, it must have a physical bodily reaction to the source of 'Trans-gendered people' - Movies cannot feel - argument is invalid.
But no - basically if it was, it would be putting it further into the light than the intended meaning "That killer is a batsh*t psycho killer who uses ladies skins to be like them". The do not do that, so it is not.