Using House of M as a 'look what happens if mutants get rights' argument is about like using Rob Liefeld's art for a course on accurate human anatomy.
Mutants are entitled to human rights, because a human mutant is still human. Mutants are mutated humans. If they were another species, they would be called something else. A mutant is so called because it has mutated but is still a member of the species. The whole reason why ignorant anti-mutant idiots in comics are characters people hate is because they're wrong and they're stupid; they are judging by external appearances, rather than by the quality of one's character, and furthermore they're not using any accurate scientific thought to differentiate between perceived species. They're just hating on something that's different, because they don't understand it and thus are afraid of it. They do it in the real world just as in the comics, it's nothing new.
As comic geeks (at least some of the people here) we really should recognise that is why X-Men was, in better-written days, an appealing comic: we ourselves were often judged by external appearances, or by petty differences from the glorified 'norm', and many of us were happier not being like everyone else, even if we had fewer friends or less social life. Being identifiably the 'uncool kids' or the outcasts, the people who are fantastic but aren't usually given a chance, has been the raison d'être of the X-titles since their inception. Anyone in any sort of minority or ostracised group could identify with their situation, which gave them an appeal that kept readers holding on for even little victories.
So this really isn't a question. Mutants are human, otherwise they would be called something else entirely. On every level, it's ludicrous to debate. And frankly, as some others have pointed out, in the Marvel Universe even anti-mutant hysteria is rather nonsensical when you have exactly the same sort of superhuman powers shown by world celebrities like the Avengers and the Fantastic Four.