As of December 9, 2016 all new domains added to Cloudflare via partners have Free SSL enabled. In order to enable Free SSL for existing customers whose domains were added prior to December 9, 2016 it's necessary to delete and re-add the domain to be provisioned automatically.
Additionally, if your domain was added using Cloudflare Partial (CNAME) set up, you must have CNAME verification records in place to verify the domain, you can use this Cloudflare API call to obtain SSL verification CNAME records to trigger the certificate to be issued.
You can check the status of the SSL certificate on the Crypto tab in the Cloudflare dashboard. Additional information can be found in our SSL FAQ.