It's really a mixed bag of reasons why especially young people and immature people (and some very mature people) don't like us; religious bias, family bias, insecurity, "Ew, that's just gross!" (honestly, I get how they feel, I personally think morbidly obese people are physically pretty gross, no offense to anyone who is or has a family member who is obese, but if you've seen the television shows about 800lbs people, it gets very, very nasty - imagine what some people naturally think of folks who want to chop off their penises.), peer pressure, or simply that it's sometimes easy for us to be the butt of jokes.
However, I think that only insecure transsexuals truly are discriminated or harassed. If someone is a constantly happy, powerful person, anyone around them, even the most passionate bigots, tend to break down and question why they are hating a happy person so much. Now, on par with what I said on another thread about how only 'ugly' or 'non-passing' Trans get picked on, I still stand by that too; I believe that the only Transpeople who are insecure even after a hormonal transition are the ones who are self-concious of their appearance and do need FFS or other improvements to complete the full picture. I believe every Transperson deserves to have a confidence so high that it's unrealistic. No Transperson should shut the door on further confidence options, because if you live life with a subdued persona even after your hormonal transition, society will target you. Whichever way a Transperson can gain a full pot of confidence, they deserve it.