And the default/largest homeserver, matrix.org, uses cloudflare, so all your data belongs to them as well.

It is disappointing that they use Cloudflare, especially since most Matrix metadata hasn't yet been moved to the end-to-end encrypted channel.

(Arathorn: is e2ee metadata still on the roadmap?)

But no, not all your data is exposed. The e2ee parts, like message content in encrypted rooms, are opaque to Cloudflare.