I was doing a fresh Flutter installation on a new Mac.

Following the instructions of Flutter doctor to install cocoapods with sudo gem install cocoapods, Cocoapods 1.8.0 was installed.
Then after running pod setup, nothing happened, and cocoapods was still not initialised.

The solution was to remove cocoapods with sudo gem uninstall cocoapods and then install Cocoapods 1.7.5 with sudo gem install cocoapods -v 1.7.5, then pod setup.

I know this is probably a Cocoapods issue, but the flutter doctor instructions need to change so new users can get Flutter to work without any trouble.