They receive a large amount of internet traffic and have the potential ability to fingerprint users and subvert privacy protections. AFAIK they don't do anything malicious, but I don't know they don't.

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.