Discrimination is a problem that we still need to solve. What may change about it in the future is that we might stumble into a situation where - to be blunt - people are discriminated against as a result of their own choices. The big problem is that while this is as indefensible as racism or anti-Semitism or anti-homosexual bigotry today, there are probably plenty of people who would not see it that way. Xenophobia doesn't need much justification for xenophobes.
What people might end up on the wrong side of these crosshairs? Possibly, people who set out to "improve" themselves - people who take advantage of biogenetic or cybernetic technologies to elevate themselves above what they once were. This sort of human modification is something I expect to see in the future; after all, it's relatively inexpensive, particularly when compared to the whole "cities on Mars" trope that is common in science fiction, and present-day technology is beginning to approach the point where it might be feasible. Consider, for a moment, digilegs.
Right now, these are innocuous; aids for cosplayers and movie producers, primarily. Nevertheless, I can easily see a time when technology has advanced to such a point where these could stop being just aids. There are people who, if the opportunity was available, wouldn't hesitate to replace their natural legs with mechanical digitigrade legs and live their lives as cyberfauns, cybercentaurs, or whatever. The idea of people identifying themselves as "non-human" is not new; otherkin, as an organized subculture, have existed for twenty years, and the concept of therianthropy has pretty much existed in one form or another since the dawn of human culture.
These people would be distinguishing themselves from "ordinary people" in a significant way, and by doing so they would make themselves targets to some of them. Given that the "improvers" might be geographically scattered, discrimination against them could be even more vociferous - and the fact that they chose this would probably encourage the sort of people who'd discriminate, that they "deserve it" for choosing to make themselves "inhuman."
The prototype for this already exists in the world to some extent - discrimination against atheists. It's the one avenue of discrimination I can think of that's based on the perception that it's the result of a choice - granted, that's often the case, but not nearly universally. Article 36 of Maryland's Bill of Rights, for example, states that an otherwise-competent witness may not "be deemed incompetent as a witness, or juror, on account of his religious belief; provided, he believes in the existence of God" - because, as we all know, the only possible reason people don't lead their lives in a manic, orgiastic whirlwind is because they're afraid of Hell. Granted, it's not nearly as harsh as racist discrimination has been in the past - but it does presage, I think, the capacity to discriminate based on an idea and not an intrinsic nature.
It's a shame, really. When I was growing up, the future always seemed like it should be the kind of place where this sort of thing didn't exist at all. Now that I'm older, I realize that the future is just the present - shinier in some ways, and dirtier in others.