I personally love Cloudflare. It's made a ton of stuff a lot easier for me as a developer. Sure, there's some downsides... but that's true with any service. (And a lot of the complaints are opt-in features that the web developer enabled)
It seems the author only has problems with Cloudflare almost completely because he uses Tor. Unfortunately, most Tor traffic is malicious (94%, by Cloudflare's count), and the whole point of Cloudflare is to prevent malicious attacks.
Anytime you do something for privacy (block ads, disable JS, use Tor), unfortunately things won't always work exactly how you expect.
Lastly, it ends with a weird conspiracy theory... "It is probably a US Government-attached intelligence agency". Okay.