If you need to connect to your origin using another protocol (SSH, FTP, SMTP, etc.) you need to do so using a record that does not have Cloudflare enabled in the DNS settings (grey cloud) or by connecting directly to the origin server’s IP address.
For example, if your domain is example.com, connect to server using a grey url like
$ ssh email@example.com
where ssh.example.com is an A record pointing to same ip as example.com.