In order for our SSL vendor to issue the certificate for your domain name, it needs to go through a vetting process. Depending on your plan this may take anywhere from 15 minutes to 24 hours (paid vs. free). You can look at the status of your cert by going to the Cloudflare settings, you may see Authorizing, Pending, or Verified.
If you have waited longer than that, your domain name may be flagged for further review. Please create a ticket letting us know and we will reach out to our SSL vendor for further analysis.