Wait, you’re suggesting they had board room discussions where they consciously, actively chose to protect and encourage ddos-for-hire sites because the threat of ddos attacks helps keep cloudflare in business?
Again, this isn't free speech -- it is the antithesis of free speech. That's called hypocrisy.
And yes, of course they cooperate with the FBI on specific cases (or, at least one specific case) of DDoS-for-hire prosecution. Not only because they are compelled to do so by law, but because they are the only company that can identify where the perpetrators are actually hosted.