In fact I would say CloudFlare are better than both GitHub and Facebook, and I am only wary of them because of their position of power and the potential they have (ie. they are a victim of their own success). Both Facebook and GitHub have shown themselves to make political decisions at the expense of their users.
To privacy-conscious users: CloudFlare is the man-in-the-middle for more and more of the Internet, potentially tracking at Google-like levels.
CloudFlare may: ... Add script to your pages to, for example, add services, Apps, or perform additional performance tracking. (Unfortunately this is opt-out rather than opt-in.)
To Tor users: CloudFlare implements a captcha to protect servers from malicious traffic; the implementation has caused tremendous annoyance in the past and the company may have been slow to address this problem.
https://news.ycombinator.com/item?id=7977780 (example complaint, 3 years ago)
https://news.ycombinator.com/item?id=11388560 (9 months ago, from cloudflare)
https://news.ycombinator.com/item?id=11404770 (the tor project response)
https://news.ycombinator.com/item?id=12122268 (6 months ago, additional discussion of tor vs. captcha)
To DDoS victims: CloudFlare protects several DDoS vendors while gaining business protecting DDoS victims, citing free speech.
To CloudFlare customers: CloudFlare has a "target on its back" and has faltered against DDoS in the past, causing outages for all of its customers. AFAIK: It's been a while.
To CloudFlare freeloaders like me: CloudFlare doesn't have much incenctive to protect its free-tier users from DDoS.
Related: Akami stopped helping DDoS'd pro-bono client Brian Krebs. https://news.ycombinator.com/item?id=12561928
In my book CloudFront easily ranks ahead of had-been "do no evil" Google's irrevocably merging it's entire history on me ex post facto. https://news.ycombinator.com/item?id=12760003