Okay, let's start at the beginning with some vocab: "cis" or "cisgender", (if I am understanding it correctly by way of context as well as this post on Feministe), means that your genetic gender and the way your mind perceives itself gender-wise match up; cisgender people are people who are not transgender or otherwise gender-queer. For a lot of people (including those who are offended by the term), being cis means you are "normal", and I think that perception is what's causing a lot of the drama in Feminist Bloglandia.
For some reason, some people just don't understand that pluralism applies to everybody. If we get to live in a pluralistic society and have whatever sexuality we feel is normal or natural, that means everyone else does. And it doesn't stop at sexuality or religion or racial issues, it extends to gender. The funny thing is that feminism started as a gender issue, yet radical feminists are the last people to get on the gender-plurality bandwagon, and stop being assholes to people whose gender doesn't fit in with the binary gender our culture has forced upon us because our biology (mostly) limits us to one or the other.
The issue is that some feminists think that trans women aren't women. They get offended at the idea of a woman who was born male using the women's restroom. They think that the woman who was born male really is still male, and so will act like a man, and of course the transwoman, who identifies as a woman, who dresses as a woman, who experiences society as a woman -- who sometimes experiences society on even worse terms that ciswomen because she gets the sexist end of the stick from men and the cissexist end of the stick from some women -- is a woman. Period.
We've got all of this shit floating around about what makes a "real" man, what makes a "real" woman; but the large and small of the whole thing is that if you identify as a man, you are a man and if you identify as a woman you are a woman; if you identify as something other than a man or a woman, you are something other than that. And believe it or not people, there are those out there who identify as neither male nor female, or as both; those people exist and they need to be acknowledged as part of society and as part of feminism. Feminism isn't just for women who were born female, who were born white, who were born middle class. Feminism is for the betterment of all women everywhere, and that happens to have a pretty cool side effect (in theory) of making the life better for everyone else who do not identify as women.
The real issue here is prejudice... and well, outright hate in some cases. We can't do this. As feminists we can't do this. Those of us who are not transgender/genderqueer need to educate ourselves rather than expecting people who are transgender/genderqueer to do it, thereby othering them (either purposefully or subconsciously). After we get educated, we need to reach out to trans and genderqueer people and tell them we are sorry for excluding them from feminism and from society. These women (and men) are women and men. They experience society differently from cis-people, but part of that is because we make them. That's not fair.
And I'll tell you something about forcing someone to experience society differently because you think they deserve it: it's not okay. Men have done it to women because "god" made them bigger and stronger. White people have done it to non-whites because "god" advanced their technology faster so they could colonize the rest of the world. Straight people have done it to gay people because someone's god somewhere said that being gay was "an abomination". And now cis feminists are doing the same fucking thing to trans and genderqueer feminists (as well as poor, nonwhite, etc feminists) because god has made it so their brains and biological gender are the same? Come on. We feminists rail against sexism in all of its forms... but when we start acting like assholes because the people we're being sexist against were born male -- this is okay?
Newsflash: it's not. Sexism is wrong. Racism is wrong. Homophobia is wrong. Transphobia is wrong. Cissexism is wrong. We can't play this game, feminism. We can't cut people out like this. It's only going to make our job as feminists harder and our world uglier for all women.
People don't get to be treated well because they were lucky enough to be born "normal"; you treat people well because it's the right thing to do.