Time to put my three yen into this discussion....
I think a point people might be missing here is that in the Marvel universe --
which this story, if not a full crossover, draws from -- there exists a
prejudice and suspicion against mutants that doesn't extend to other types of
super-powered humans. Characters like the Fantastic Four or the Avengers have
never really been harrassed the way that the X-men have. (Others like Spiderman
and the Hulk have been, but of course for vastly different reasons.) This is the
simple result of having different dramatic needs in different comic series that
co-exist in the same fictional continuity, but it's not hard to justify it in
story terms. Just the existence of someone like Magneto, who views mutants as
the master race, who is openly working to subjugate the rest of humanity to
mutants and has the power to make it possible, would be enough to cause an
outbreak of fear and suspicion among the general public.
What's missing, I think, is some way for Akane in this story to be identified as
a mutant as opposed to just some random super-type. If you can establish that
there's some sort of distinctive feature that a mutant (and no one else) has,
something that Akane and all the people who are turning hostile to her can
recognize, then I think it would solve a lot of the problems that people are
having with this.
Gary