It depends, really. Real-life bigotries have a lot of history around them, and narratives built up over centuries. Contrary to popular belief, it's not actually the case that people see others who are different and automatically go 'ew, different people; let's bully them!' 
If you were to suddenly drop superpowered people in the midst of our current modern society, for instance, I honestly don't think people would suddenly decide to hate on them, at least not until they've figured out how they fit in to their already existing narratives about people and society. (In fact, you could probably test this by going to a hate forum or smth and asking how they'd feel about superpowered people; I'm willing to bet they'd be like 'I'd be cool with superpowered people, why wouldn't I be?')
The role that differences actually play is they introduce power dynamics over time, as two different kinds of people interact, memories and anecdotes accumulate, power struggles happen, narratives get established, etc. So if superpowered people have existed this whole time, you will probably end up with them being discriminated against, or conversely you might end up with them at the top of the hierarchy and in a position of power over the non-superpowered 
So yeah, it could eventually go in this direction, but I wouldn't say people would automatically decide to privilege them any more than they would automatically decide to hate them.
It all depends on initial conditions; who won the physical/cultural power struggles at the start (establishing a power dynamic which tends to snowball and become further entrenched over time). This could be a function of how common superpowered people are, how the powered/nonpowered difference interact with other demographic differences, and probably a whole bunch of other factors XD
There's a difference in how people hate smart/talented people though, vs how people hate racial/sexual/gender/religious minorities 