People keep saying "You can't compare the SH registration act to registering alcohol!" And yet, the same sort of reasoning can be applied to the counter-argument where people keep saying that the license to own guns and drive cars is proof that superheroes need a license to use their powers. Well, the major flaw in comparing the registration of superheroes to the registration of vehicle drivers and gun owners is that people who drive cars and buy guns aren't out there voluntarily risking their own lives to save ours, every single day. There is no comparison; these are people giving their free time and their lives to perform a much-needed community service, not people who use these dangerous "privileges" for recreation and travel.
If some heroes obviously need to be trained, then train them, fine. But when you go around labelling the entire community of heroes -- several of whom have saved the world many times over -- like criminals, that's really just accusing people of and prosecuting people for crimes that they hadn't even committed. And there's no way to defend that.
Of course superheroes don't trust the government; the Marvel U government can't be trusted! You think that's paranoid and oversensitive? Look at how the government in the Marvel universe actually works: they have traditionally and constantly lambasted superheroes and persecuted them for the flimsiest of excuses. And yet they are often completely laissez-faire on their attitude towards supervillains and will often let these murderers and rapists off with a slap on the wrist. Agent Hill wants to know why Spider-Man hasn't gotten rid of the Green Goblin? I want to know why the hell Agent Hill hasn't gotten rid of the Green Goblin.
They'll hunt constantly for Daredevil, and yet they'll give Magneto an entire nation of his own. They constantly strive to make the superheroes' jobs harder and make the supervillains' jobs easier. If you were a superhero in this sort of world, would you trust the government either? How long would it be before your public identity gets passed on to the nearest widow-maker villain with some sort of "agreement" with SHIELD?
There is a distinct and blatant line between a hero and a villain, and this act is just the latest in a long tradition of the Marvel universe's need to blur that line. Which is fine from the meta-narrative perspective -- aka the perspective of writers to write an interesting story and the perspective of readers to read it -- but it's certainly not okay from the perspective of characters who actually live in this world. Fans sometimes bring up the cliche that the main difference between the DCU and the Marvel U is that the DCU has godlike superheroes while the Marvel has more humane ones; I, however, will argue that the only substantial difference between the two universes nowadays is that the DCU treats their heroes with reverence while the Marvel U treats their heroes with suspicion.