I hate patent trolls with a passion, but these non-practicing entities are are just another negative by-product of what has devolved to be a negative system. Patents originally existed to protect inventors. Today, like in other legal systems, they have very little to do with justice and a lot to do with "whoever has the gold makes the rules". As such, while I definitely side with CloudFlare, it does seem like a complaint of "not fair, they are manipulating the rotten system better than us"
3. They don't seem to be against patents, just against non-practicing entities. Did you even read the article?