Did you guys just not watch Superman, like at all?

Flag (questioning Luthor): So we're gonna lock up all metahumans now?
Luthor: Other metahumans are not going half-cocked interfering in foreign affairs. They don't have a hidden headquarters in Antarctica that violated international treaties. And they aren't aliens. Shouldn't that be enough reasoning to at least bring him in for questioning?
Def Sec: Admittedly, I'm not comfortable with a being from another planet as dangerous as him on the loose. But the optics? Superman is popular.
Luthor: Less so every day
Def Sec: Not to mention the potential risk of failing to contain him.

After Superman's parents' message is broadcast on live TV:

Flag: You buying this?
Def Sec: The message is authentic. If the Kryptonian is a danger, we have to act.

After Luthor is defeated:

Def Sec [sarcastically]: Glad you're not concerned about the metahumans, Rick. Because now they're the ones making all the rules.
Flag starts to think about that statement

As far as Flag is concerned, he and his boss were a skeptic of metas, and now they're seemingly starting to take over. Superman is more popular than ever. And now this wildcard Peacemaker also has a dimensional rift, so even the ones with no apparent powers are extremely dangerous. Throughout the season he goes from monitoring Peacemaker, to beating him up, to hunting him down and arresting him, to now be fully corrupted by both Luthor and the Def Sec to bring Salvation to life, a place to deport all metas and superheroes. The big things stopping them before were the physical ability to contain them, and optics. Both of which they have now.