They are to be protected. We have some patents that would come close to bitcoin and have spoken to some of the groups in btc to ensure it’s all safe there. Patent protection is about protecting open source from our perspective, it’s how we evolve society and that includes SAFE and all related projects.
There was a ton of fear and weird stuff said a while back, but it’s all in very good hands and in a good place. I am the sole inventor on all the patents and it would be hard for anyone to get their hands on them and use them against innovation, if not impossible. At the moment they will protect against larger players with proprietary code and massive marketing budgets though. so good 
[edit some more info here Cointelegraph: Clearing the Air Over MaidSafe’s Patent Request: An Interview with COO Nick Lambert ]