Cadmus Operation 66 wasn't just for the literal meta-humans; those who simply donned a mask went into hiding with them. Of course, the directive of the order wasn't for people to go into hiding. It was for them all to be "apprehended." At least, that was the word Waller had given the public, anyway. The heroes knew what she really meant.
The government tracked down all the villains, too. They even got Lex Luthor, on tax evasion of all things. The fact that he didn't get a trial probably helped.
The only difference between the hunt of the heroes and the hunt of the villains was that, when it came to the bad guys, they called it what it was: execution.
Superman turned himself over willingly, boy-scout that he was. His reasoning was that a show of good faith would make them go easier; and even if it didn't, he still had that Kryptonian invincibility, so they couldn't kill him. Only, he didn't know about the vast stores of Kryptonite the government had. Cadmus had managed to get enough to make an entire facility out of it. No one heard from Superman after that.
Gotham and Central were the last cities to allow the soldiers onto their streets. Gotham had fought through the common folk protesting, and Commissioner Gordon holding the government off through a mix of the police force and bureaucratic red tape. Even then, they only lasted two weeks against Cadmus. Gordon tried to be their inside man, and help the Bats get away before the task force struck next, but he was caught after a month. Barbara wouldn't talk for a week when she found out.
Central City fought back by hiding the Flashes in their respective houses, but after the fifth family was arrested for helping them, they fled to the Watch Tower.
The only people who survived were the Bats, the Flashes, the Atlantians, The League of Shadows, and M'gaan. The Bats because, well, they were all trained by Batman; the Flashes because they were too fast to catch; The Atlantians because they were technically a sovereign nation; The League because they were all scary ninja assassins, and traveled in huge packs; and M'gaan because the government's Martian detection systems weren't calibrated for White Martians.
On the last meeting of the Justice League (and the Team) everyone paired up before they all went radio silent. It wasn't the smartest move, strategically, but not even Batman argued. Misery loves company, after all.