I think Cloudflare did think it was a dangerous site, but they would really prefer not having the responsibility of being the arbiter of what can and cannot be hosted, as well as all of the negative publicity that comes with being so. At the same time, I believe they believe that current legal process surrounding how things like this are handles are so woefully underdeveloped that turning a blind eye is not being neutral, it's being irresponsible.
Taking downs sites like this hurts the view of infrastructure neutrality, so I'm sure it's not done lightly, even when someone goes against their policy.
Most customers do not have means of being harmful to the utility by their actions of using the utility itself. If for example your use of the power network caused damage to the network and effected other customers than you can believe you would get an immediate cut off order until the situation was remediated.
Sites behind cloudflare, in theory (lots of debate here) could be considered harmful to cloudflare's network by their behavior, hence presenting a risk to the network and its customers.
Taking downs sites like this hurts the view of infrastructure neutrality, so I'm sure it's not done lightly, even when someone goes against their policy.