The content you host will only be blocked from being indexed if you decide to use a service that blocks indexing. If you host your content on other people's services, then you never had the power to make that decision anyway.
If you want your content to be indexed, simply don't use Cloudflare. Host your own servers. Use a different CDN if you want the benefits of Cloudflare's networks.
If you want your content to be indexed, simply don't use Cloudflare. Host your own servers. Use a different CDN if you want the benefits of Cloudflare's networks.