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They basically generate the SSL certificate for your domain for you. Their SSL CA partner (GlobalSign IIRC) is basically trusting them with it since they manage their certificate and the domain owner is trusting Cloudflare (this can also be checked in Whois). So you just activate SSL in the options and bam, your site works with SSL within a couple of minutes.

BTW: they use certificates with multiple SANs, so many different domains in the same certificate (and without SNI). This allows to terminate SSL on a single box for many different domains/customers. If you look at certificates details, you will see many unrelated domains in the SAN list.

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