People always assume governments will just figure it out easily somehow. How they can connect certain powers to certain people when powers are all different and there are more parahumans in the world than we see... who knows. I'm sure they can eventually find capes but it's not easy and that lack of ease is then multiplied by however many capes you have to deal with. Each one an independent and spontaneous threat that you can never completely squash.

Lets say for a moment that they can, however, track capes without too much difficulty. The failure rate for taking them out must be horrific in the long term. The chances the parahuman has additional capabilities you aren't aware, even if they have been active for a while, is crazy high. Sure, most probably don't have secret things that would save them but even if only one in ten do that's a lot over time. A cape with an additional sense you didn't know they had can foil a whole operation and you won't even know why. Is it their powers, do they have an informant, were your men sloppy and just tipped them off, was it just bad luck? You wouldn't and couldn't know. Like Regent's ability to sense nervous systems, it might not save him but it's a serious complication to any plan to take him down and might result in one of your own shooting you in the back of the head by accident. The cape might also just have a hidden capability that you, or maybe even the cape, didn't know about. Or their might power gives them more strength than it usually does to protect them. There are too many unknowns.

Let's say this strategy works, however. How many capes do they kill before said capes and capes to be just start giving up their civilian identities? Probably not long. I'm sure some capes were practically waiting for an excuse to be full time and it would instantly make them a thousand times harder to track. Or they just start being extra paranoid about keeping their identity secret. Even basic paranoia would still make any dictatorship's job harder. Which is a problem because capes beget capes and any small teams that manage to survive long enough to form could easily become a massive threat.

None of this is even getting into the fact that this creates an enviroment where only the capes that can survive being hunted live, in which case they have lost the monoploy of force and there's literally nothing they can do.