Enough with the conspiracy theories...
In the days before Cloudflare existed - indeed, very nearly the days before services like Cloudflare's existed, being as it was almost exacly the time Prolexic got off the ground - my site was DDoSed by an organised crime gang, and our ISP's 'help' was black-holing us entirely, on the grounds that the DDoS against us was taking down all the other clients in the datacentre. To be honest, I understood their decision then and I'd understand it again now.
So while on the one hand, obviously it's bad that Cloudflare did this, all the "oh noes, I had no idea a network provider could do such a thing!" hand wringing is a nonsense. At the end of the day, what else do you expect to happen? All the other customers to salute and go down on the ship with you?