Back to the OP (since I just discovered this thread)...
I really believe the problems that transgendered people have in integrating with society is down to societal issues, and that the broader context has to be examined in order to reach the particular. I think it's down to evolution. Hear me out...

Societies evolve over time. Survival of the fittest, so to speak. If your societal structure manages to unite more people than another, eventually your culture will dominate the surrounding cultures, either by conquest or by subversion. To do this, a common religion, creed, language, and/or identity is required. The culture, to survive, must have some fundamental level of cohesion. On a macro scale, this can be managed through laws and policies from a government or church body, on a micro scale this is managed by strict adherents in the populace.
So, a powerful, successful, cohesive culture *must* encourage conformity on some level or another. The way this is done is through the use of people's social desire to fit in, to belong (carrot) and a fear of being excluded (stick). The beliefs of people who are fully indoctrinated in such a culture and who are naturally are predisposed to desire conformity are rewarded by their culture for being upstanding adherents.
However, to thrive, a culture must also change with the times in order to survive environmental (geo-political now) changes. Thus, a certain degree of non-conformity *must* exists, and this role is filled by people who think in a more independent fashion... however, this is general. There are certain unifying cultural ideas that are preserved for the most part even in those people. And, people being what they are, there is a sort of bell-curve in how they respond to world-challenging ideas. On one end, with few adherents, is complete anarchy, where everyone is free to do anything they wish regardless of the consequences. On the other is complete conservatives who want nothing to change ever; new ideas, to them, are evil, even if it's just a new color of wax for their cars. Everyone else is scattered along the curve, with most in the middle.
The trouble, in my opinion, comes from the fact that gender roles are enshrined in our society (I blame the patriarchy, but this isn't about feminism, so I'll leave it there). They have historically been imposed on us since birth. There is a small percentage of the population who doesn't fit their assigned gender, but to *this* culture that is nearly unthinkable. To another culture, such as the Navajo, it's no big deal, accepted and dealt with. Unfortunately the Western European culture has nearly completely overwhelmed that of the native tribes... so this tenet, that men are men and do manly things and women are women and do womanly things, is enshrined as a pillar of society. Without knowing why, women and men, girls and boys, believe that these roles are correct. To avoid standing out, to gain acceptance, they will conform. To "help" others integrate, they will bully, tease, hurt, bribe, or any other tactic they think might work to get *them* to conform too.
The only way to change that (and it is changing, at least in the US) is to educate people... let them see that trans people aren't a threat to their country and their way of life. To come out in numbers and show ourselves to be the men and women and others that we are.
It's a slow battle. It has been said it takes three generations to create lasting change. We're almost there for lesbian and gay rights, and to some degree our wagon is hitched to theirs. There is promise; these are exciting times.
Much love,
Robin