So first things first Let's Encrypt and Cloudflare are amazing, but just enabling the Cloudflare cloud and Let's Encrypt makes it impossible to auto renew domains. This rule change will allow you to auto renew with Let's Encrypt and make everyone happy.
This is because Let's Encrypt will do a ACME challenge on your domain on each renewal attempt, and with the default Cloudflare settings it will fail.
The simple solution is to enable a simple page rule on Cloudflare. This is a simple rule to disable SSL force on the ACME requests.
Now here is a copy of the rule, and just disable SSL.