I'm having the same issue but disabling DNSSEC didn't change anything for me. Cloudflare's help site says No for everything except the bottom section, regardless.
I also cross referenced the official docs/guide against Ben Dews' guide (which I followed to setup the Pihole) and Ben's guide did not mention putting 127.0.0.1#5053 as the upstream DNS. However, when I did that the DNS server quit responding and pages would no longer load.