CloudFlare's customers can choose whether the backhaul, between CloudFlare and their own web servers, is HTTP, HTTPS with a CloudFlare issued private certicate, or HTTPS using publicly trusted certs from the Web PKI.

If you choose either of the latter two options, bad guys can't MITM you, the middle option has the benefit that they can't even MITM you by subverting a public CA (since only CloudFlare's own certs are trusted) the latter option has the benefit that you can "just" switch off CloudFlare and your site now works as an ordinary HTTPS site with no changes, if you ever want to do that.