Why should I use P2P communication ?
P2P communication is mainly aimed for application that require that multiple client speak to each other. One of the basic example of that kind of application would be a chat. All the information that are sent between the client won't have to pass through the server. It reduces traffic and load on your server since you are now sending and receiving less data while doing the same thing.
Why shouldn't I use P2P communication ?
There are 2 principle obstacle to P2P communication. Network infrastructure and Flash support. If you are inside a corporate or school network, there's a strong chance nobody will be able to connect to you because of the way the network you are in is made. As for the Flash support, it isn't supported on some mobile platform and even tough there is a larger proportion of the Internet user that have it, some don't have it for various of reasons ( OS support, they don't have admin rights on their machine, etc. ).
What about security ?
The RTMFP protocol informations are quite vague or hidden, so it's hard to say how secure the protocol is, but from what Adobe has written so far it seems that the information that is exchanged between the client is encrypted.
The only certitude that you can have is that the information that a client will receive will be from untrusted source (an other client, not the server), so you have to implement the same information checking that your server would have, but on the client.