Mutant issue....

No, I've seen that 5000 superhumans somewhere as well (not counting the players, of course). Plus, it makes sense, the Rikti Wars state that most meta-humans gathered at Paragon City for the final assault on the aliens, regardless of whether they were heroes or villains. Paragon Wiki lists the Alpha team as having 1000 supers, and the Omega team as having 100 mages. That's 1100, a rough estimate of Primal Earth's meta-human numbers in 2001. Of course, not every meta-human fought in the wars, and some that did weren't officially counted (the Circle of Thorns fought underground, for instance). Plus, by 2012, meta-human numbers appear to have increased with the growing number of Powers Division, redeemed Warshades, Paragon Protectors, Vahzilok, Freakshow, the Infected, etc, but they wouldn't soar so much in just 11 years. 5000 overall, mostly split between Paragon City and Rogue Isles sounds about right. There might be more registered heroes, but that probably includes the guy with a pepper-spray can wearing a pantyhose on his head.

You see signs of fear and paranoia everywhere in Paragon City. You have Vanguard billboards saying "They're still among us", you have Chris Jenkins advertising cheap lawsuits to anyone who got hurt by supers, you have Citizens for Medi-corp complaining that heroes are given special treatment, you have government-sponsored organizations like Malta actively gunning down every meta-human they find (hero or villain), you have Crey Industries appealing for a complete dismantle of non-regulated hero organizations like the Freedom Corps, Wyvern and Longbow, and that's just off the top of my head.

If you follow Marvel's logic, mutants are a special case among meta-humans - their abilities tend to first manifest during puberty, triggered by stressful situations and often accompanied with uncontrollable bursts of power, which can dangerous to anyone around them. Plus, unlike City of Heroes, Marvel lists millions of mutants worldwide, not hundreds, so it's fair to assume the chance of a mutant teenager going time-bomb in school is pretty high - no wonder parents would fear this fenomenon. Do you know how Cyclops found out he was a mutant in Ultimate X-men? He inadvertedly cut his foster parents in half with an optic blast after a heated argument. Add to that the words of their politicians, scientists, priests, reporters, radio talk-show hosts, even a Brotherhood of Evil Mutants, all saying mutants will one day replace humankind, and you've got the makings of a lynching mob.

Spider-man and the other freak-science supers would be viewed differently by the general population. First, unlike mutants, they're rare, freak occurences, and if they go "bad", well, the "good" freaks who wear capes will arrest them. Second, it can happen to anyone, but it mostly happens to adults or late teens, almost never to children, so at least freaks tend to grow up normal, unlike mutants who find out they're different (some would say superior) by the age of twelve. Third, there's almost no recorded instances of freaks going supernova when they first get their powers, which tend to grow gradually rather than suddenly manifest in full force. Fourth, and perhaps most important, freaks almost always become either heroes or villains, so they're either adored or hated, unlike mutant teenagers who will often try to cling to their old lives as if nothing happened.

In Marvel universe, people love the Beast, mutant or not, he's also a hero and a former Avenger who saved the world countless times. They hate Gambit, Rogue and Magneto because those three were at one time villains as well, what's to stop them from going rogue again? As to most nameless mutant teenagers out there trying to go about their own business, people view them with suspicion even if they didn't hurt anyone when their powers manifested, much like any person they know is carrying a concealed unregistered firearm - they might be forced to pick a side one day, hero or villain, and being undecided is just one step closer to villainy.

Like it or not, introducing mutants to the world means creating a dystopic society. Normal humans can't become mutants, are mostly defenseless against mutants, and are therefore treated as second-class citizens until the law grants them unique rights to protect them. This is no different from the lower middle ages, when a select group of petty nobles had free reign to dictate their will to the peasant majority. Their word was absolute, and no one would think to stop them, in fact, no one could - there's no way a starving village with no weapons could stand up against a army of trained soldiers.

City of Heroes doesn't list that many mutants, so the problem is bogus here - even if they went evil, mutants are both outnumbered and outgunned by the other origins. If that weren't true, if non-mutant meta-humans numbered in the hundreds and mutants in the millions like in Marvel comics, that'd be a different story.