How do you remove the root CA certificate that fiddler installs

Since Fiddler 4.6.1.5 the GUI is a bit different.

Go to Tools -> Fiddler Options -> HTTPS. Then click the "Actions" button and then "Reset All Certificates"

It will popup a message that it could take a while but it's really quick. Approve all popups and there you go.

Pay attention not to re-approve the certificate again (when I did it the message for approving the certificates popped up when I finished to approve all the popups.)

In Fiddler go to Tools » Options » HTTPS.
Then uncheck Decrypt HTTPS traffic and run Actions » Remove Interception Certificates.

This will remove all Fiddler certs from the Windows certificate store.

Background:
Fiddler is obviously using a kind of white hat "man in the middle" approach to decrypt and inspect any HTTPS traffic. To do that, it needs its own certs to be trusted. Therefore leaving Decrypt HTTPS traffic checked but removing the Fiddler certs as proposed in other answers does not make a lot of sense, as Fiddler can't decrypt then anyway.

Either of two ways:

1) Disable HTTPS decryption and click the button titled "Remove Interception Certificates"

2) Open CertMgr.msc, open the Personal and Trusted Stores, and use the Delete key on the root.