The issue goes back to Teh Magical Masquerade, and there're always 2 sides on the Magical side:
- The "Magic is for everyone, share, make everyone happy side and don't be a jerk!" side. (think of the mostly Campy Negima chapters)
- The "Magic is for the elite and born to magic, shut up and get better genes/mana/circuits/blood/whatever into the family!" side. (think of the mostly Dark Negima chapters, ohai F/SN)
There is the fact that discrimination also exists in the Magical World, but it's more based on abilities since those in the know can be of different/mixed races/species (werewolves, tengu, demon, etc) or just plain going with the classic "being a descendant of so-and-so badass =~= some kind of royalty".
We've also been shown there is still slavery and other means of societal control in the Magical World that the "Old World" doesn't normally (publicly) partake of in general because of human rights, differing social moral subsets, etc.
Another of the reasons the Masquerade is kept up is that not all the muggles will believe in magic:
-those that do are more tolerant and/or interested in it and will eventually be in contact with it (ohai Mahora academy and most of it's students/faculty);
- and those that don't, think it's either some ruse, technology or some such activity to cover up something bigger (conspiracy theorists, non magical people, haters that couldn't get/do any magic, religious nutz, non-magical military states, etc).
Although both worlds seem to have the same core issues... some people want power/control, and will do whatever they can to get it.