So if we assume maximum tx size is 2kb, the longest possible comment, then an accounnt c annot put more than 2.9mb per day on the chain. However, what other methods of flood protection does the system have? If every available RPC is used, and transactions are multiply broadcast across all available RPC's, and they all relay that into the gossip p2p between rpc, seed and witness nodes, what is going to stop the servers from being overwhelmed?

I think nothing. I think, if someone wants to take down this network, script kiddy level skills are all that's required. Besides that, once the nodes are being flooded, what other vulnerabilities are going to open?

The design assumes no adversaries at all. This seems like a pretty dumb assumption with all the astroturfing that goes on, and the trolling against anyone who raises a valid concern.