I actually read this Federalist article to see what the argument was. It all lands on one central premise:

Actually, no.
So, maybe this is news, but a telephone call has (at minimum) two people on the call. So if you're spying on a non-US citizen - say Kislyak - and Kislyak has a phone call then it means you're also listening to the second person too. It's an absurdity to argue that it's somehow improper to keep listening to the call because Michael Flynn is on the other end of the phone. That's precisely the kind of information you're spying on Kislyak to find out.
The logical leaps conservative media makes to protect their guys are sometimes surreal.