There's nothing stopping them from releasing their own root CA or their users accepting a self-signed cert. A pain in the ass, absolutely, but not insurmountable.
Interesting. It appears to be kept in an extension, the regular CN field is for .cloudflare-dns.com:
Not Critical
DNS Name: .cloudflare-dns.com
IP Address: 1.1.1.1
IP Address: 1.0.0.1
DNS Name: cloudflare-dns.com
IP Address: 2606:4700:4700::1111
IP Address: 2606:4700:4700::1001