Middleboxes no longer considered harmful

I had a hard time following this paper, since the main motivation for it i didn't truely understand. From what i've read, it seems like instead of trying to prevent NAT boxes or other middle boxes from existing within the network, they tried to setup a framework that allowed the NAT boxes to co-exist. One of the main methods of doing that was to basically give every unique internet host a unique identifier. However, besides the fact that it breaks the network layer infrastructure, i don't really see how firewalls and NAT boxes are harmful, infact, since i use a router i home, it seems to me that they are more beneficial then harmful, just because they can protect a user from being directly connected to the network, and can filter out harmful traffic. As a result, i didn't really understand the point behind this paper.