Dokku has a Let's Encrypt plugin which works behind Cloudflare. There's just a little bit of chicken-and-egg setup involved.
Let's Encrypt needs to connect back to your server to validate ownership of your domain. You can't have Cloudflare's "full" TLS mode enabled when you're doing first-time validation, because in "full" mode Cloudflare will error out, failing to establish a TLS connection to your not-yet-TLS backend server.
You could disable "full (strict)" TLS mode in Cloudflare, but then you'll take all your sites down: Dokku does HTTP -> HTTPS redirects on all sites configured with TLS, and will thus reject the non-TLS inbound connections from Cloudflare's networks. Or more accurately, it'll receive an inbound HTTP request from Cloudflare's servers, return a redirect to HTTPS, which Cloudflare will pass on to the client, but the client is already at an HTTPS URL, so the client will enter an infinite redirect loop.
You can get around all this during first-time setup by disabling Cloudflare's proxying behavior on your domain while you get Let's Encrypt set up on Dokku. After it's set up, you can turn Cloudflare proxying on, and cert renewals should work fine, since Let's Encrypt validation checks routed through Cloudflare can still establish end-to-end TLS while your certs remain valid.