In my opinion, it's not the word so much as the context it's used in.
Most words can be given different associations, or implications, depending on how they're used. And it's those associations and implications that provoke emotional reaction. In a split second, not only do we see the word, but the mind analyses who said it, what sort of a person they are, why they said it, and what they hope to achieve by saying it. And I think that all contributes to a person's reaction to the word, as well as their own experiences, their self-confidence or self-esteem, understanding of what the word means to them, if/when they would use it and what their own intent would be in its use.
Words may just be words, but the neurological and emotional processes involved in a reaction to a word can be complex. So it's not as simple as saying "Oh, it's just a word, it shouldn't bother you." Words can cut deeper than a knife. And often, the negative connotations attached to a word don't just disappear when the word is said in an entirely innocent, or even positive context.
For me personally, the word '->-bleeped-<-' is de-humanising. It reduces a person to nothing more than a condition they suffer from, and often one which they do everything in their power to try and keep in the background, to try to live their lives as just as any other person.
To me it's akin to calling someone with diabetes a "Diabety", or someone with asthma an "Asthmy". Quite aside from the hate and scorn often attatched to the word by people with transphobia... it just makes very little sense, in my opinion, to use it in any context as a label for someone, even if it's 'reclaimed' by people dealing with transsexuality. I much prefer the term 'person' or 'human being'.